Starting phenix.real_space_refine on Mon Sep 30 11:31:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vj7_43276/09_2024/8vj7_43276.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vj7_43276/09_2024/8vj7_43276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vj7_43276/09_2024/8vj7_43276.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vj7_43276/09_2024/8vj7_43276.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vj7_43276/09_2024/8vj7_43276.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vj7_43276/09_2024/8vj7_43276.cif" } resolution = 4.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 119 5.16 5 C 16153 2.51 5 N 4167 2.21 5 O 4736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 25175 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6269 Classifications: {'peptide': 796} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 772} Chain breaks: 2 Chain: "B" Number of atoms: 6257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6257 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 771} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 6268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6268 Classifications: {'peptide': 796} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 19, 'TRANS': 771} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 6253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 6253 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 771} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'A1AB5': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'A1AB5': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'A1AB5': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'A1AB5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.75, per 1000 atoms: 0.59 Number of scatterers: 25175 At special positions: 0 Unit cell: (121.83, 161.82, 190.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 119 16.00 O 4736 8.00 N 4167 7.00 C 16153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.32 Conformation dependent library (CDL) restraints added in 3.2 seconds 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5852 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 32 sheets defined 48.1% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain 'A' and resid 22 through 37 Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 116 through 128 removed outlier: 4.616A pdb=" N ALA A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 142 removed outlier: 3.808A pdb=" N GLY A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 139 through 142' Processing helix chain 'A' and resid 143 through 157 Processing helix chain 'A' and resid 174 through 187 removed outlier: 3.747A pdb=" N ARG A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.634A pdb=" N LYS A 234 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.555A pdb=" N THR A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 302 Processing helix chain 'A' and resid 325 through 335 Processing helix chain 'A' and resid 390 through 390 No H-bonds generated for 'chain 'A' and resid 390 through 390' Processing helix chain 'A' and resid 391 through 394 removed outlier: 3.537A pdb=" N THR A 394 " --> pdb=" O GLU A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 394' Processing helix chain 'A' and resid 410 through 414 removed outlier: 4.485A pdb=" N GLU A 413 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.773A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 545 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 628 removed outlier: 3.532A pdb=" N ARG A 599 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 642 removed outlier: 3.716A pdb=" N SER A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 757 Processing helix chain 'A' and resid 757 through 767 Processing helix chain 'A' and resid 768 through 771 removed outlier: 3.896A pdb=" N GLY A 771 " --> pdb=" O TYR A 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 768 through 771' Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 818 removed outlier: 3.831A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 81 through 93 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 143 through 157 Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 172 through 185 removed outlier: 3.532A pdb=" N GLU B 185 " --> pdb=" O PHE B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.847A pdb=" N GLY B 230 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.682A pdb=" N THR B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 302 Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.690A pdb=" N GLU B 328 " --> pdb=" O GLY B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.540A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.754A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.631A pdb=" N MET B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 625 removed outlier: 3.703A pdb=" N THR B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 642 removed outlier: 3.671A pdb=" N LYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 677 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 792 through 817 removed outlier: 3.832A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 37 Processing helix chain 'C' and resid 54 through 68 Processing helix chain 'C' and resid 81 through 93 Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 143 through 157 Processing helix chain 'C' and resid 169 through 173 Processing helix chain 'C' and resid 174 through 187 removed outlier: 3.876A pdb=" N ARG C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 231 through 236 removed outlier: 4.127A pdb=" N LYS C 234 " --> pdb=" O ASP C 231 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN C 236 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.642A pdb=" N THR C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 303 Processing helix chain 'C' and resid 324 through 335 removed outlier: 4.327A pdb=" N GLU C 328 " --> pdb=" O GLY C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.816A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.704A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 545 Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 627 Processing helix chain 'C' and resid 636 through 642 removed outlier: 3.931A pdb=" N SER C 640 " --> pdb=" O ALA C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.556A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 677 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.554A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 757 Processing helix chain 'C' and resid 757 through 767 Processing helix chain 'C' and resid 792 through 820 removed outlier: 3.806A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 37 Processing helix chain 'D' and resid 54 through 68 Processing helix chain 'D' and resid 81 through 93 Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 139 through 142 Processing helix chain 'D' and resid 143 through 157 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 172 through 187 removed outlier: 3.683A pdb=" N LYS D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 232 through 236 Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.949A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 302 Processing helix chain 'D' and resid 324 through 335 removed outlier: 4.270A pdb=" N GLU D 328 " --> pdb=" O GLY D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 414 removed outlier: 3.963A pdb=" N GLU D 413 " --> pdb=" O LYS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.893A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.704A pdb=" N GLU D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.717A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 545 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 624 Processing helix chain 'D' and resid 637 through 641 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 677 Processing helix chain 'D' and resid 685 through 697 removed outlier: 3.594A pdb=" N LYS D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 742 through 757 Processing helix chain 'D' and resid 757 through 767 Processing helix chain 'D' and resid 792 through 817 removed outlier: 3.782A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 50 removed outlier: 7.136A pdb=" N GLN A 13 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N PHE A 74 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLY A 15 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 164 removed outlier: 7.558A pdb=" N PHE A 133 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE A 163 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TYR A 135 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LYS A 132 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ILE A 193 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA A 134 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASP A 195 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU A 136 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE A 245 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 338 through 340 removed outlier: 3.549A pdb=" N VAL A 338 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 340 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 346 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.453A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA7, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.114A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.541A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET A 721 " --> pdb=" O ILE A 504 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 42 through 50 removed outlier: 6.215A pdb=" N ILE B 12 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N HIS B 46 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE B 14 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASP B 48 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY B 16 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU B 50 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE B 18 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 10.500A pdb=" N ALA B 72 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLN B 13 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N PHE B 74 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLY B 15 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE B 73 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 161 through 164 removed outlier: 6.084A pdb=" N TYR B 135 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE B 245 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE B 358 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR B 373 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE B 360 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AB3, first strand: chain 'B' and resid 440 through 444 removed outlier: 6.433A pdb=" N VAL B 396 " --> pdb=" O ILE B 474 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB6, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.827A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 498 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 730 " --> pdb=" O LEU B 498 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 704 through 705 removed outlier: 4.128A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE B 504 " --> pdb=" O MET B 721 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET B 721 " --> pdb=" O ILE B 504 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.445A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 42 through 50 removed outlier: 10.250A pdb=" N ALA C 72 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N GLN C 13 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N PHE C 74 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLY C 15 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 159 through 164 removed outlier: 7.467A pdb=" N PHE C 133 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ILE C 163 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR C 135 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LYS C 132 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ILE C 193 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA C 134 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASP C 195 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU C 136 " --> pdb=" O ASP C 195 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE C 245 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN C 359 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS C 364 " --> pdb=" O PRO C 368 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 373 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 346 through 347 Processing sheet with id=AC3, first strand: chain 'C' and resid 395 through 399 removed outlier: 6.523A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AC5, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AC6, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.013A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 500 through 503 removed outlier: 6.442A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 42 through 50 removed outlier: 6.103A pdb=" N ILE D 12 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N HIS D 46 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE D 14 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ASP D 48 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU D 50 " --> pdb=" O GLY D 16 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE D 18 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 10.654A pdb=" N ALA D 72 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLN D 13 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N PHE D 74 " --> pdb=" O GLN D 13 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLY D 15 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE D 96 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 159 through 164 removed outlier: 7.619A pdb=" N PHE D 133 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ILE D 163 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR D 135 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE D 245 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 338 through 340 Processing sheet with id=AD2, first strand: chain 'D' and resid 441 through 444 Processing sheet with id=AD3, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AD4, first strand: chain 'D' and resid 489 through 491 removed outlier: 3.513A pdb=" N THR D 736 " --> pdb=" O ASP D 490 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 646 through 649 removed outlier: 6.490A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 1188 hydrogen bonds defined for protein. 3438 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: 9.36 Time building geometry restraints manager: 7.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8027 1.34 - 1.46: 6267 1.46 - 1.58: 11220 1.58 - 1.70: 1 1.70 - 1.83: 195 Bond restraints: 25710 Sorted by residual: bond pdb=" C2 A1AB5 C1401 " pdb=" N1 A1AB5 C1401 " ideal model delta sigma weight residual 1.275 1.450 -0.175 2.00e-02 2.50e+03 7.70e+01 bond pdb=" C2 A1AB5 D1302 " pdb=" N1 A1AB5 D1302 " ideal model delta sigma weight residual 1.275 1.446 -0.171 2.00e-02 2.50e+03 7.35e+01 bond pdb=" C2 A1AB5 C1403 " pdb=" N1 A1AB5 C1403 " ideal model delta sigma weight residual 1.275 1.445 -0.170 2.00e-02 2.50e+03 7.20e+01 bond pdb=" C2 A1AB5 A1302 " pdb=" N1 A1AB5 A1302 " ideal model delta sigma weight residual 1.275 1.444 -0.169 2.00e-02 2.50e+03 7.14e+01 bond pdb=" C3 A1AB5 C1403 " pdb=" N2 A1AB5 C1403 " ideal model delta sigma weight residual 1.290 1.451 -0.161 2.00e-02 2.50e+03 6.46e+01 ... (remaining 25705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.25: 34669 5.25 - 10.49: 58 10.49 - 15.74: 3 15.74 - 20.99: 0 20.99 - 26.24: 8 Bond angle restraints: 34738 Sorted by residual: angle pdb=" C THR D 394 " pdb=" N VAL D 395 " pdb=" CA VAL D 395 " ideal model delta sigma weight residual 121.97 132.98 -11.01 1.00e+00 1.00e+00 1.21e+02 angle pdb=" C4 A1AB5 A1302 " pdb=" C3 A1AB5 A1302 " pdb=" N2 A1AB5 A1302 " ideal model delta sigma weight residual 116.15 89.91 26.24 3.00e+00 1.11e-01 7.65e+01 angle pdb=" C4 A1AB5 C1403 " pdb=" C3 A1AB5 C1403 " pdb=" N2 A1AB5 C1403 " ideal model delta sigma weight residual 116.15 90.12 26.03 3.00e+00 1.11e-01 7.53e+01 angle pdb=" C4 A1AB5 D1302 " pdb=" C3 A1AB5 D1302 " pdb=" N2 A1AB5 D1302 " ideal model delta sigma weight residual 116.15 90.41 25.74 3.00e+00 1.11e-01 7.36e+01 angle pdb=" C10 A1AB5 C1401 " pdb=" C3 A1AB5 C1401 " pdb=" C4 A1AB5 C1401 " ideal model delta sigma weight residual 118.62 142.97 -24.35 3.00e+00 1.11e-01 6.59e+01 ... (remaining 34733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 13871 17.86 - 35.73: 1090 35.73 - 53.59: 248 53.59 - 71.45: 46 71.45 - 89.31: 46 Dihedral angle restraints: 15301 sinusoidal: 6136 harmonic: 9165 Sorted by residual: dihedral pdb=" C GLU B 705 " pdb=" N GLU B 705 " pdb=" CA GLU B 705 " pdb=" CB GLU B 705 " ideal model delta harmonic sigma weight residual -122.60 -141.46 18.86 0 2.50e+00 1.60e-01 5.69e+01 dihedral pdb=" CA LYS D 393 " pdb=" C LYS D 393 " pdb=" N THR D 394 " pdb=" CA THR D 394 " ideal model delta harmonic sigma weight residual 180.00 146.25 33.75 0 5.00e+00 4.00e-02 4.56e+01 dihedral pdb=" CA PHE C 546 " pdb=" C PHE C 546 " pdb=" N SER C 547 " pdb=" CA SER C 547 " ideal model delta harmonic sigma weight residual -180.00 -148.68 -31.32 0 5.00e+00 4.00e-02 3.92e+01 ... (remaining 15298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 3822 0.139 - 0.277: 7 0.277 - 0.416: 0 0.416 - 0.555: 0 0.555 - 0.693: 1 Chirality restraints: 3830 Sorted by residual: chirality pdb=" CA GLU B 705 " pdb=" N GLU B 705 " pdb=" C GLU B 705 " pdb=" CB GLU B 705 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CG LEU A 184 " pdb=" CB LEU A 184 " pdb=" CD1 LEU A 184 " pdb=" CD2 LEU A 184 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CA PRO D 593 " pdb=" N PRO D 593 " pdb=" C PRO D 593 " pdb=" CB PRO D 593 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.02e-01 ... (remaining 3827 not shown) Planarity restraints: 4395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 628 " -0.579 9.50e-02 1.11e+02 2.60e-01 4.12e+01 pdb=" NE ARG C 628 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG C 628 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 628 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 628 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 506 " 0.052 5.00e-02 4.00e+02 7.39e-02 8.75e+00 pdb=" N PRO C 507 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 507 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 507 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 704 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C LEU B 704 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU B 704 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU B 705 " -0.013 2.00e-02 2.50e+03 ... (remaining 4392 not shown) Histogram of nonbonded interaction distances: 0.67 - 1.52: 4 1.52 - 2.36: 57 2.36 - 3.21: 24121 3.21 - 4.05: 64723 4.05 - 4.90: 117897 Warning: very small nonbonded interaction distances. Nonbonded interactions: 206802 Sorted by model distance: nonbonded pdb=" CD GLU D 705 " pdb=" OE2 GLU D1301 " model vdw 0.673 3.270 nonbonded pdb=" OE2 GLU D 705 " pdb=" OE2 GLU D1301 " model vdw 0.804 3.040 nonbonded pdb=" OE2 GLU D 705 " pdb=" CD GLU D1301 " model vdw 0.902 3.270 nonbonded pdb=" CD GLU D 705 " pdb=" CD GLU D1301 " model vdw 1.373 3.500 nonbonded pdb=" CG GLU D 705 " pdb=" OE2 GLU D1301 " model vdw 1.576 3.440 ... (remaining 206797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 504 or (resid 505 and (name N or name CA or nam \ e C or name O or name CB )) or resid 506 through 772 or (resid 773 and (name N o \ r name CA or name C or name O or name CB )) or resid 774 through 817 or (resid 8 \ 18 through 819 and (name N or name CA or name C or name O or name CB )) or resid \ 1301)) selection = (chain 'B' and (resid 10 through 504 or (resid 505 and (name N or name CA or nam \ e C or name O or name CB )) or resid 506 through 772 or (resid 773 and (name N o \ r name CA or name C or name O or name CB )) or resid 774 through 819 or resid 13 \ 01)) selection = (chain 'C' and (resid 10 through 504 or (resid 505 and (name N or name CA or nam \ e C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1402)) selection = (chain 'D' and (resid 10 through 772 or (resid 773 and (name N or name CA or nam \ e C or name O or name CB )) or resid 774 through 819 or resid 1301)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 54.790 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.175 25710 Z= 0.445 Angle : 0.777 26.235 34738 Z= 0.405 Chirality : 0.043 0.693 3830 Planarity : 0.006 0.260 4395 Dihedral : 14.498 89.314 9428 Min Nonbonded Distance : 0.673 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.54 % Favored : 96.21 % Rotamer: Outliers : 0.48 % Allowed : 9.99 % Favored : 89.54 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.54 (0.15), residues: 3164 helix: 1.47 (0.14), residues: 1417 sheet: -0.25 (0.29), residues: 357 loop : -0.59 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 605 HIS 0.004 0.001 HIS A 214 PHE 0.029 0.002 PHE A 296 TYR 0.017 0.001 TYR A 533 ARG 0.003 0.000 ARG C 594 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 737 time to evaluate : 2.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.7979 (m-30) cc_final: 0.7350 (t0) REVERT: A 382 LEU cc_start: 0.8657 (pp) cc_final: 0.8410 (tp) REVERT: A 463 MET cc_start: 0.8509 (mmm) cc_final: 0.8247 (mmt) REVERT: A 518 LEU cc_start: 0.9037 (mt) cc_final: 0.8045 (mt) REVERT: A 539 VAL cc_start: 0.9615 (t) cc_final: 0.8852 (m) REVERT: A 573 ILE cc_start: 0.8896 (tt) cc_final: 0.8376 (tt) REVERT: A 584 PHE cc_start: 0.8762 (t80) cc_final: 0.8377 (t80) REVERT: A 585 MET cc_start: 0.8776 (mmt) cc_final: 0.8543 (mmm) REVERT: A 611 ILE cc_start: 0.9562 (mm) cc_final: 0.9250 (mm) REVERT: A 613 ILE cc_start: 0.9338 (mm) cc_final: 0.8530 (tp) REVERT: A 661 ARG cc_start: 0.9077 (mmt180) cc_final: 0.8405 (ttp80) REVERT: A 670 MET cc_start: 0.9208 (mtp) cc_final: 0.8882 (mtp) REVERT: A 789 LEU cc_start: 0.8254 (tp) cc_final: 0.7925 (tp) REVERT: A 805 LEU cc_start: 0.9004 (tt) cc_final: 0.8621 (mm) REVERT: B 25 GLU cc_start: 0.8563 (mp0) cc_final: 0.8239 (mp0) REVERT: B 175 GLU cc_start: 0.9483 (mp0) cc_final: 0.9233 (pm20) REVERT: B 214 HIS cc_start: 0.8185 (p90) cc_final: 0.7560 (p-80) REVERT: B 255 VAL cc_start: 0.8989 (t) cc_final: 0.8779 (p) REVERT: B 362 GLU cc_start: 0.8847 (tt0) cc_final: 0.8454 (mm-30) REVERT: B 378 ASP cc_start: 0.8851 (m-30) cc_final: 0.8639 (m-30) REVERT: B 514 VAL cc_start: 0.7643 (t) cc_final: 0.7395 (p) REVERT: B 533 TYR cc_start: 0.8185 (t80) cc_final: 0.7856 (t80) REVERT: B 534 ILE cc_start: 0.9102 (mt) cc_final: 0.8710 (tt) REVERT: B 540 LEU cc_start: 0.8580 (tp) cc_final: 0.8258 (tp) REVERT: B 573 ILE cc_start: 0.8803 (tp) cc_final: 0.8030 (tp) REVERT: B 601 VAL cc_start: 0.9151 (t) cc_final: 0.8651 (p) REVERT: B 608 PHE cc_start: 0.8953 (t80) cc_final: 0.8564 (t80) REVERT: B 614 SER cc_start: 0.9682 (m) cc_final: 0.9362 (t) REVERT: B 620 LEU cc_start: 0.8761 (tp) cc_final: 0.8519 (tt) REVERT: B 798 ILE cc_start: 0.8976 (mt) cc_final: 0.8324 (tt) REVERT: C 79 LYS cc_start: 0.9010 (ptmm) cc_final: 0.8581 (pttm) REVERT: C 107 HIS cc_start: 0.7998 (m90) cc_final: 0.7540 (m-70) REVERT: C 161 THR cc_start: 0.9336 (m) cc_final: 0.9047 (p) REVERT: C 188 LYS cc_start: 0.8885 (mttt) cc_final: 0.8337 (tptp) REVERT: C 200 LYS cc_start: 0.9249 (mmmt) cc_final: 0.8782 (tttt) REVERT: C 284 LEU cc_start: 0.8889 (tp) cc_final: 0.8684 (mt) REVERT: C 518 LEU cc_start: 0.8994 (mt) cc_final: 0.6804 (mt) REVERT: C 540 LEU cc_start: 0.8718 (tp) cc_final: 0.8507 (tp) REVERT: C 584 PHE cc_start: 0.8691 (t80) cc_final: 0.8283 (t80) REVERT: C 585 MET cc_start: 0.8663 (mmt) cc_final: 0.8262 (mmm) REVERT: C 601 VAL cc_start: 0.9332 (t) cc_final: 0.8967 (p) REVERT: C 611 ILE cc_start: 0.9511 (mm) cc_final: 0.9075 (mm) REVERT: C 613 ILE cc_start: 0.9236 (mm) cc_final: 0.7969 (tp) REVERT: C 617 THR cc_start: 0.9557 (m) cc_final: 0.9290 (t) REVERT: C 630 VAL cc_start: 0.8177 (m) cc_final: 0.7937 (p) REVERT: C 638 ASP cc_start: 0.9022 (m-30) cc_final: 0.8003 (m-30) REVERT: C 659 PHE cc_start: 0.8972 (m-80) cc_final: 0.8741 (m-10) REVERT: C 703 LEU cc_start: 0.9251 (mt) cc_final: 0.8704 (mt) REVERT: C 789 LEU cc_start: 0.8294 (tp) cc_final: 0.7989 (mt) REVERT: C 805 LEU cc_start: 0.8886 (tt) cc_final: 0.8570 (mm) REVERT: D 18 PHE cc_start: 0.8807 (m-80) cc_final: 0.8295 (m-10) REVERT: D 138 ASP cc_start: 0.7437 (t0) cc_final: 0.7105 (t0) REVERT: D 165 VAL cc_start: 0.9248 (p) cc_final: 0.8642 (p) REVERT: D 175 GLU cc_start: 0.8676 (mp0) cc_final: 0.8458 (mp0) REVERT: D 177 TYR cc_start: 0.8786 (m-80) cc_final: 0.8488 (m-80) REVERT: D 208 VAL cc_start: 0.8648 (t) cc_final: 0.8247 (t) REVERT: D 232 LEU cc_start: 0.8876 (pt) cc_final: 0.8676 (pp) REVERT: D 293 THR cc_start: 0.8132 (m) cc_final: 0.7856 (p) REVERT: D 373 TYR cc_start: 0.7879 (p90) cc_final: 0.7038 (p90) REVERT: D 378 ASP cc_start: 0.8582 (m-30) cc_final: 0.7942 (m-30) REVERT: D 463 MET cc_start: 0.4924 (mmp) cc_final: 0.3479 (mtt) REVERT: D 502 ILE cc_start: 0.8193 (mt) cc_final: 0.7987 (mp) REVERT: D 514 VAL cc_start: 0.8101 (t) cc_final: 0.7839 (p) REVERT: D 521 LEU cc_start: 0.9361 (mt) cc_final: 0.8992 (mt) REVERT: D 534 ILE cc_start: 0.8954 (mt) cc_final: 0.8552 (tt) REVERT: D 587 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8436 (mp10) REVERT: D 601 VAL cc_start: 0.9387 (t) cc_final: 0.9020 (p) REVERT: D 610 LEU cc_start: 0.9305 (tp) cc_final: 0.8859 (tt) REVERT: D 611 ILE cc_start: 0.9668 (mm) cc_final: 0.9388 (mm) REVERT: D 612 ILE cc_start: 0.9631 (mm) cc_final: 0.9224 (tt) REVERT: D 614 SER cc_start: 0.9613 (m) cc_final: 0.9234 (t) REVERT: D 624 LEU cc_start: 0.8959 (mt) cc_final: 0.8551 (mm) REVERT: D 795 VAL cc_start: 0.9249 (p) cc_final: 0.8733 (m) outliers start: 13 outliers final: 3 residues processed: 745 average time/residue: 0.3858 time to fit residues: 438.7537 Evaluate side-chains 421 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 418 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 0.4980 chunk 239 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 161 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 chunk 247 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 150 optimal weight: 9.9990 chunk 184 optimal weight: 20.0000 chunk 286 optimal weight: 5.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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: 0.7336 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25710 Z= 0.296 Angle : 0.687 10.471 34738 Z= 0.361 Chirality : 0.045 0.195 3830 Planarity : 0.005 0.089 4395 Dihedral : 5.205 66.187 3519 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.45 % Favored : 96.37 % Rotamer: Outliers : 0.22 % Allowed : 3.17 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.15), residues: 3164 helix: 1.41 (0.14), residues: 1452 sheet: -0.51 (0.27), residues: 387 loop : -0.49 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 526 HIS 0.009 0.002 HIS B 214 PHE 0.041 0.002 PHE D 237 TYR 0.020 0.002 TYR D 647 ARG 0.016 0.001 ARG C 628 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 473 time to evaluate : 2.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8246 (m-30) cc_final: 0.7916 (t0) REVERT: A 178 ARG cc_start: 0.9270 (mtt90) cc_final: 0.8831 (mmt180) REVERT: A 214 HIS cc_start: 0.8521 (p-80) cc_final: 0.8251 (p90) REVERT: A 527 MET cc_start: 0.7491 (mmp) cc_final: 0.6423 (mmp) REVERT: A 539 VAL cc_start: 0.9527 (t) cc_final: 0.9250 (p) REVERT: A 541 PHE cc_start: 0.7449 (t80) cc_final: 0.7002 (t80) REVERT: A 573 ILE cc_start: 0.8592 (tt) cc_final: 0.8292 (tp) REVERT: A 613 ILE cc_start: 0.8872 (mm) cc_final: 0.8405 (tp) REVERT: A 661 ARG cc_start: 0.9127 (mmt180) cc_final: 0.8497 (ttp80) REVERT: A 674 MET cc_start: 0.9028 (ptp) cc_final: 0.8741 (ptp) REVERT: B 17 LEU cc_start: 0.9028 (tp) cc_final: 0.8630 (tp) REVERT: B 25 GLU cc_start: 0.8717 (mp0) cc_final: 0.8487 (mp0) REVERT: B 175 GLU cc_start: 0.9617 (mp0) cc_final: 0.9232 (pm20) REVERT: B 188 LYS cc_start: 0.9314 (tmmt) cc_final: 0.9066 (tptt) REVERT: B 292 MET cc_start: 0.7515 (ppp) cc_final: 0.7183 (ppp) REVERT: B 378 ASP cc_start: 0.9008 (m-30) cc_final: 0.8766 (m-30) REVERT: B 518 LEU cc_start: 0.9132 (mt) cc_final: 0.8594 (mt) REVERT: B 533 TYR cc_start: 0.8597 (t80) cc_final: 0.7918 (t80) REVERT: B 611 ILE cc_start: 0.9647 (mm) cc_final: 0.9347 (tp) REVERT: B 612 ILE cc_start: 0.9553 (mm) cc_final: 0.9111 (tt) REVERT: B 614 SER cc_start: 0.9479 (m) cc_final: 0.9230 (t) REVERT: B 708 MET cc_start: 0.9076 (ttp) cc_final: 0.8797 (ptm) REVERT: B 789 LEU cc_start: 0.8709 (tp) cc_final: 0.8248 (tp) REVERT: B 799 LEU cc_start: 0.9378 (tp) cc_final: 0.9076 (tt) REVERT: C 74 PHE cc_start: 0.8474 (t80) cc_final: 0.8244 (t80) REVERT: C 107 HIS cc_start: 0.8581 (m90) cc_final: 0.8267 (m90) REVERT: C 132 LYS cc_start: 0.8780 (ttpp) cc_final: 0.8379 (ttmm) REVERT: C 161 THR cc_start: 0.9252 (m) cc_final: 0.8966 (p) REVERT: C 188 LYS cc_start: 0.9415 (mttt) cc_final: 0.9003 (tptp) REVERT: C 196 CYS cc_start: 0.8179 (m) cc_final: 0.5876 (m) REVERT: C 200 LYS cc_start: 0.9525 (mmmt) cc_final: 0.8907 (ttpt) REVERT: C 361 MET cc_start: 0.7342 (mpp) cc_final: 0.6759 (mpp) REVERT: C 479 LEU cc_start: 0.9355 (tp) cc_final: 0.9014 (tp) REVERT: C 518 LEU cc_start: 0.9190 (mt) cc_final: 0.8074 (mt) REVERT: C 527 MET cc_start: 0.7359 (mmp) cc_final: 0.6892 (mmp) REVERT: C 540 LEU cc_start: 0.8857 (tp) cc_final: 0.8421 (tp) REVERT: C 613 ILE cc_start: 0.8627 (mm) cc_final: 0.8243 (tp) REVERT: C 670 MET cc_start: 0.8937 (ptp) cc_final: 0.8721 (ptp) REVERT: C 705 GLU cc_start: 0.8198 (pm20) cc_final: 0.7826 (pm20) REVERT: C 795 VAL cc_start: 0.9555 (p) cc_final: 0.9322 (p) REVERT: C 805 LEU cc_start: 0.9088 (tt) cc_final: 0.8864 (mm) REVERT: D 17 LEU cc_start: 0.9459 (mt) cc_final: 0.9253 (mt) REVERT: D 83 ASN cc_start: 0.8844 (p0) cc_final: 0.8324 (p0) REVERT: D 93 HIS cc_start: 0.8702 (m-70) cc_final: 0.8201 (m-70) REVERT: D 113 MET cc_start: 0.8209 (tpt) cc_final: 0.6922 (tpp) REVERT: D 138 ASP cc_start: 0.8294 (t0) cc_final: 0.7944 (t0) REVERT: D 177 TYR cc_start: 0.9046 (m-80) cc_final: 0.8423 (m-80) REVERT: D 193 ILE cc_start: 0.9302 (mp) cc_final: 0.9078 (mm) REVERT: D 284 LEU cc_start: 0.9187 (mm) cc_final: 0.8624 (mm) REVERT: D 293 THR cc_start: 0.8327 (m) cc_final: 0.8038 (p) REVERT: D 378 ASP cc_start: 0.8728 (m-30) cc_final: 0.7929 (m-30) REVERT: D 380 MET cc_start: 0.7919 (tmm) cc_final: 0.7655 (tmm) REVERT: D 463 MET cc_start: 0.5374 (mmp) cc_final: 0.4947 (mmm) REVERT: D 496 MET cc_start: 0.6165 (ppp) cc_final: 0.5732 (ppp) REVERT: D 525 ILE cc_start: 0.8621 (mt) cc_final: 0.8375 (mt) REVERT: D 600 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8606 (mm) REVERT: D 614 SER cc_start: 0.9585 (m) cc_final: 0.9255 (t) REVERT: D 795 VAL cc_start: 0.8846 (p) cc_final: 0.8424 (m) outliers start: 6 outliers final: 1 residues processed: 474 average time/residue: 0.3671 time to fit residues: 275.2479 Evaluate side-chains 323 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 321 time to evaluate : 2.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 159 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 238 optimal weight: 0.0070 chunk 195 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 287 optimal weight: 0.0050 chunk 310 optimal weight: 9.9990 chunk 256 optimal weight: 0.9990 chunk 285 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 230 optimal weight: 8.9990 overall best weight: 0.9616 ------------------------------------------------------------------------------- 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: 0.7309 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25710 Z= 0.174 Angle : 0.568 10.373 34738 Z= 0.296 Chirality : 0.042 0.222 3830 Planarity : 0.004 0.062 4395 Dihedral : 4.653 65.421 3519 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.26 % Favored : 96.55 % Rotamer: Outliers : 0.15 % Allowed : 2.54 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.15), residues: 3164 helix: 1.58 (0.14), residues: 1450 sheet: -0.43 (0.27), residues: 388 loop : -0.33 (0.18), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 158 HIS 0.009 0.001 HIS B 214 PHE 0.031 0.002 PHE A 36 TYR 0.024 0.001 TYR A 286 ARG 0.005 0.000 ARG D 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 422 time to evaluate : 2.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8168 (m-30) cc_final: 0.7832 (t0) REVERT: A 178 ARG cc_start: 0.9267 (mtt90) cc_final: 0.8944 (ptp-110) REVERT: A 463 MET cc_start: 0.8973 (mmm) cc_final: 0.8766 (mmt) REVERT: A 527 MET cc_start: 0.7452 (mmp) cc_final: 0.6677 (mmp) REVERT: A 613 ILE cc_start: 0.8930 (mm) cc_final: 0.8467 (tp) REVERT: A 661 ARG cc_start: 0.9096 (mmt180) cc_final: 0.8467 (ttp80) REVERT: A 789 LEU cc_start: 0.8502 (tp) cc_final: 0.8150 (tp) REVERT: B 17 LEU cc_start: 0.8844 (tp) cc_final: 0.8546 (tp) REVERT: B 25 GLU cc_start: 0.8691 (mp0) cc_final: 0.8468 (mp0) REVERT: B 113 MET cc_start: 0.8997 (mpp) cc_final: 0.8635 (mpp) REVERT: B 175 GLU cc_start: 0.9571 (mp0) cc_final: 0.9190 (pm20) REVERT: B 225 LEU cc_start: 0.8732 (mt) cc_final: 0.8487 (mt) REVERT: B 292 MET cc_start: 0.7576 (ppp) cc_final: 0.7098 (ppp) REVERT: B 378 ASP cc_start: 0.8993 (m-30) cc_final: 0.8747 (m-30) REVERT: B 517 PHE cc_start: 0.7892 (p90) cc_final: 0.7689 (p90) REVERT: B 518 LEU cc_start: 0.9133 (mt) cc_final: 0.8693 (tt) REVERT: B 533 TYR cc_start: 0.8489 (t80) cc_final: 0.8056 (t80) REVERT: B 585 MET cc_start: 0.8154 (mmm) cc_final: 0.7919 (mmt) REVERT: B 612 ILE cc_start: 0.9415 (mm) cc_final: 0.8873 (tt) REVERT: B 614 SER cc_start: 0.9409 (m) cc_final: 0.9162 (t) REVERT: B 709 ASN cc_start: 0.8446 (t0) cc_final: 0.8061 (t0) REVERT: B 789 LEU cc_start: 0.8561 (tp) cc_final: 0.8155 (tp) REVERT: B 798 ILE cc_start: 0.8657 (mt) cc_final: 0.8197 (tt) REVERT: C 113 MET cc_start: 0.8562 (mmp) cc_final: 0.8141 (mmm) REVERT: C 161 THR cc_start: 0.9362 (m) cc_final: 0.9083 (p) REVERT: C 214 HIS cc_start: 0.9095 (p-80) cc_final: 0.8889 (p-80) REVERT: C 292 MET cc_start: 0.9332 (ppp) cc_final: 0.8948 (ppp) REVERT: C 479 LEU cc_start: 0.9374 (tp) cc_final: 0.8925 (tp) REVERT: C 527 MET cc_start: 0.7256 (mmp) cc_final: 0.6842 (mmp) REVERT: C 705 GLU cc_start: 0.8117 (pm20) cc_final: 0.7805 (pm20) REVERT: C 789 LEU cc_start: 0.8616 (tp) cc_final: 0.8386 (tp) REVERT: C 805 LEU cc_start: 0.9094 (tt) cc_final: 0.8855 (mm) REVERT: D 33 MET cc_start: 0.8795 (ppp) cc_final: 0.8386 (ppp) REVERT: D 83 ASN cc_start: 0.8950 (p0) cc_final: 0.8478 (p0) REVERT: D 93 HIS cc_start: 0.8679 (m-70) cc_final: 0.8208 (m-70) REVERT: D 177 TYR cc_start: 0.9078 (m-80) cc_final: 0.8512 (m-80) REVERT: D 193 ILE cc_start: 0.9320 (mp) cc_final: 0.9022 (mm) REVERT: D 196 CYS cc_start: 0.8704 (m) cc_final: 0.8236 (p) REVERT: D 201 VAL cc_start: 0.9577 (t) cc_final: 0.9198 (t) REVERT: D 293 THR cc_start: 0.8290 (m) cc_final: 0.8035 (p) REVERT: D 378 ASP cc_start: 0.8715 (m-30) cc_final: 0.7732 (m-30) REVERT: D 463 MET cc_start: 0.5322 (mmp) cc_final: 0.5024 (mmp) REVERT: D 496 MET cc_start: 0.5941 (ppp) cc_final: 0.5558 (ppp) REVERT: D 517 PHE cc_start: 0.7848 (p90) cc_final: 0.7519 (p90) REVERT: D 527 MET cc_start: 0.7861 (mtp) cc_final: 0.7337 (ttm) REVERT: D 612 ILE cc_start: 0.9606 (mm) cc_final: 0.9191 (tt) REVERT: D 614 SER cc_start: 0.9453 (m) cc_final: 0.9052 (t) REVERT: D 629 MET cc_start: 0.7787 (tpp) cc_final: 0.7170 (mmm) REVERT: D 795 VAL cc_start: 0.8727 (p) cc_final: 0.8452 (m) outliers start: 4 outliers final: 1 residues processed: 423 average time/residue: 0.3484 time to fit residues: 238.7058 Evaluate side-chains 315 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 314 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 284 optimal weight: 0.4980 chunk 216 optimal weight: 3.9990 chunk 149 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 193 optimal weight: 8.9990 chunk 288 optimal weight: 6.9990 chunk 305 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 273 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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: 0.6027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25710 Z= 0.308 Angle : 0.665 9.797 34738 Z= 0.352 Chirality : 0.044 0.190 3830 Planarity : 0.005 0.067 4395 Dihedral : 5.039 61.933 3519 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.24 % Favored : 95.58 % Rotamer: Outliers : 0.11 % Allowed : 2.80 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.37 (0.15), residues: 3164 helix: 1.18 (0.14), residues: 1470 sheet: -0.68 (0.27), residues: 385 loop : -0.43 (0.18), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP D 158 HIS 0.011 0.001 HIS D 219 PHE 0.024 0.002 PHE B 181 TYR 0.025 0.002 TYR A 77 ARG 0.006 0.001 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 361 time to evaluate : 3.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ILE cc_start: 0.9372 (mm) cc_final: 0.8832 (tp) REVERT: A 113 MET cc_start: 0.9234 (mpp) cc_final: 0.8821 (mpp) REVERT: A 140 ASP cc_start: 0.8210 (m-30) cc_final: 0.8006 (t0) REVERT: A 195 ASP cc_start: 0.8661 (t0) cc_final: 0.8356 (t0) REVERT: A 214 HIS cc_start: 0.8982 (p-80) cc_final: 0.8750 (p-80) REVERT: A 463 MET cc_start: 0.8851 (mmm) cc_final: 0.8590 (mmm) REVERT: A 527 MET cc_start: 0.7475 (mmp) cc_final: 0.6508 (mmm) REVERT: A 540 LEU cc_start: 0.8905 (tp) cc_final: 0.8702 (tp) REVERT: A 541 PHE cc_start: 0.7643 (t80) cc_final: 0.7159 (t80) REVERT: A 573 ILE cc_start: 0.8676 (tt) cc_final: 0.8089 (tp) REVERT: A 661 ARG cc_start: 0.9122 (mmt180) cc_final: 0.8751 (tmm160) REVERT: A 789 LEU cc_start: 0.8677 (tp) cc_final: 0.8231 (tp) REVERT: B 25 GLU cc_start: 0.8873 (mp0) cc_final: 0.8645 (mp0) REVERT: B 113 MET cc_start: 0.9070 (mpp) cc_final: 0.8799 (mpp) REVERT: B 175 GLU cc_start: 0.9555 (mp0) cc_final: 0.9198 (pm20) REVERT: B 292 MET cc_start: 0.8026 (ppp) cc_final: 0.7615 (ppp) REVERT: B 378 ASP cc_start: 0.9127 (m-30) cc_final: 0.8838 (m-30) REVERT: B 533 TYR cc_start: 0.8398 (t80) cc_final: 0.7863 (t80) REVERT: B 709 ASN cc_start: 0.8386 (t0) cc_final: 0.7997 (t0) REVERT: B 798 ILE cc_start: 0.8722 (mt) cc_final: 0.8425 (tt) REVERT: C 113 MET cc_start: 0.8794 (mmp) cc_final: 0.8244 (mmp) REVERT: C 292 MET cc_start: 0.9315 (ppp) cc_final: 0.8998 (ppp) REVERT: C 442 LEU cc_start: 0.9172 (mt) cc_final: 0.8948 (mt) REVERT: C 479 LEU cc_start: 0.9361 (tp) cc_final: 0.9053 (tp) REVERT: C 518 LEU cc_start: 0.8720 (mt) cc_final: 0.8492 (mt) REVERT: C 527 MET cc_start: 0.7409 (mmp) cc_final: 0.6915 (mmp) REVERT: C 540 LEU cc_start: 0.8754 (tp) cc_final: 0.8447 (tp) REVERT: C 789 LEU cc_start: 0.8727 (tp) cc_final: 0.8501 (tp) REVERT: D 17 LEU cc_start: 0.9478 (mt) cc_final: 0.9261 (mt) REVERT: D 33 MET cc_start: 0.8947 (ppp) cc_final: 0.8577 (ppp) REVERT: D 83 ASN cc_start: 0.9109 (p0) cc_final: 0.8515 (p0) REVERT: D 93 HIS cc_start: 0.8963 (m-70) cc_final: 0.8470 (m-70) REVERT: D 113 MET cc_start: 0.8535 (tpt) cc_final: 0.7344 (tpp) REVERT: D 177 TYR cc_start: 0.9282 (m-10) cc_final: 0.8817 (m-80) REVERT: D 193 ILE cc_start: 0.9315 (mp) cc_final: 0.9045 (mm) REVERT: D 284 LEU cc_start: 0.9203 (mm) cc_final: 0.8657 (mm) REVERT: D 378 ASP cc_start: 0.8822 (m-30) cc_final: 0.7952 (m-30) REVERT: D 463 MET cc_start: 0.5715 (mmp) cc_final: 0.5248 (mmm) REVERT: D 527 MET cc_start: 0.7984 (mtp) cc_final: 0.7548 (mtp) REVERT: D 799 LEU cc_start: 0.9147 (mm) cc_final: 0.8927 (tt) outliers start: 3 outliers final: 0 residues processed: 362 average time/residue: 0.3319 time to fit residues: 194.7563 Evaluate side-chains 265 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 254 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 260 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 155 optimal weight: 0.5980 chunk 274 optimal weight: 0.0060 chunk 77 optimal weight: 1.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- 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: 0.7456 moved from start: 0.6176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25710 Z= 0.166 Angle : 0.563 10.838 34738 Z= 0.293 Chirality : 0.042 0.209 3830 Planarity : 0.004 0.080 4395 Dihedral : 4.615 69.043 3519 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.73 % Favored : 96.11 % Rotamer: Outliers : 0.04 % Allowed : 2.10 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 3164 helix: 1.40 (0.14), residues: 1474 sheet: -0.57 (0.26), residues: 399 loop : -0.37 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 158 HIS 0.003 0.001 HIS D 93 PHE 0.020 0.001 PHE C 541 TYR 0.017 0.001 TYR A 286 ARG 0.004 0.000 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 371 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ILE cc_start: 0.9444 (mm) cc_final: 0.8907 (tp) REVERT: A 140 ASP cc_start: 0.8270 (m-30) cc_final: 0.7964 (t0) REVERT: A 463 MET cc_start: 0.8928 (mmm) cc_final: 0.8705 (mmm) REVERT: A 527 MET cc_start: 0.7399 (mmp) cc_final: 0.6614 (mmm) REVERT: A 661 ARG cc_start: 0.9052 (mmt180) cc_final: 0.8533 (ttp80) REVERT: A 798 ILE cc_start: 0.9330 (mt) cc_final: 0.8843 (tt) REVERT: B 17 LEU cc_start: 0.8884 (tp) cc_final: 0.8648 (mm) REVERT: B 25 GLU cc_start: 0.8875 (mp0) cc_final: 0.8590 (mp0) REVERT: B 93 HIS cc_start: 0.8645 (m90) cc_final: 0.8444 (m-70) REVERT: B 113 MET cc_start: 0.9087 (mpp) cc_final: 0.8777 (mpp) REVERT: B 124 LEU cc_start: 0.9668 (mm) cc_final: 0.9390 (mm) REVERT: B 175 GLU cc_start: 0.9547 (mp0) cc_final: 0.9158 (pm20) REVERT: B 292 MET cc_start: 0.7992 (ppp) cc_final: 0.7572 (ppp) REVERT: B 378 ASP cc_start: 0.9074 (m-30) cc_final: 0.8814 (m-30) REVERT: B 533 TYR cc_start: 0.8485 (t80) cc_final: 0.8045 (t80) REVERT: B 612 ILE cc_start: 0.9401 (mm) cc_final: 0.9022 (tt) REVERT: B 614 SER cc_start: 0.9188 (p) cc_final: 0.8656 (t) REVERT: B 670 MET cc_start: 0.8689 (mtt) cc_final: 0.8468 (mmt) REVERT: B 708 MET cc_start: 0.9052 (ttp) cc_final: 0.8689 (ptm) REVERT: B 709 ASN cc_start: 0.8287 (t0) cc_final: 0.7844 (t0) REVERT: B 798 ILE cc_start: 0.8600 (mt) cc_final: 0.8329 (tt) REVERT: C 113 MET cc_start: 0.8825 (mmp) cc_final: 0.8338 (mmp) REVERT: C 292 MET cc_start: 0.9302 (ppp) cc_final: 0.9033 (ppp) REVERT: C 361 MET cc_start: 0.7066 (mpp) cc_final: 0.6822 (mpp) REVERT: C 479 LEU cc_start: 0.9386 (tp) cc_final: 0.8999 (tp) REVERT: C 527 MET cc_start: 0.7253 (mmp) cc_final: 0.6922 (mmp) REVERT: C 540 LEU cc_start: 0.8740 (tp) cc_final: 0.8492 (tp) REVERT: D 33 MET cc_start: 0.8974 (ppp) cc_final: 0.8704 (ppp) REVERT: D 83 ASN cc_start: 0.9051 (p0) cc_final: 0.8503 (p0) REVERT: D 93 HIS cc_start: 0.8904 (m-70) cc_final: 0.8431 (m-70) REVERT: D 151 ASP cc_start: 0.9482 (m-30) cc_final: 0.9258 (t0) REVERT: D 177 TYR cc_start: 0.9198 (m-10) cc_final: 0.8663 (m-80) REVERT: D 193 ILE cc_start: 0.9207 (mp) cc_final: 0.8958 (mm) REVERT: D 231 ASP cc_start: 0.8530 (t0) cc_final: 0.8135 (t0) REVERT: D 378 ASP cc_start: 0.8729 (m-30) cc_final: 0.7791 (m-30) REVERT: D 463 MET cc_start: 0.5521 (mmp) cc_final: 0.5066 (mmm) REVERT: D 518 LEU cc_start: 0.8628 (mp) cc_final: 0.8341 (mt) REVERT: D 527 MET cc_start: 0.7837 (mtp) cc_final: 0.7461 (mtp) REVERT: D 612 ILE cc_start: 0.9545 (mm) cc_final: 0.9242 (tt) REVERT: D 614 SER cc_start: 0.9244 (p) cc_final: 0.8872 (t) REVERT: D 795 VAL cc_start: 0.8704 (p) cc_final: 0.8396 (m) REVERT: D 798 ILE cc_start: 0.8812 (mt) cc_final: 0.8106 (tt) outliers start: 1 outliers final: 0 residues processed: 371 average time/residue: 0.3482 time to fit residues: 213.9588 Evaluate side-chains 276 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 102 optimal weight: 9.9990 chunk 275 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 305 optimal weight: 5.9990 chunk 253 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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: 0.7548 moved from start: 0.6847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25710 Z= 0.252 Angle : 0.610 11.128 34738 Z= 0.320 Chirality : 0.043 0.198 3830 Planarity : 0.004 0.080 4395 Dihedral : 4.765 64.881 3519 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.30 % Favored : 95.54 % Rotamer: Outliers : 0.04 % Allowed : 1.66 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.44 (0.15), residues: 3164 helix: 1.26 (0.14), residues: 1479 sheet: -0.77 (0.26), residues: 394 loop : -0.39 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 526 HIS 0.010 0.001 HIS A 214 PHE 0.020 0.002 PHE D 517 TYR 0.020 0.001 TYR A 77 ARG 0.006 0.000 ARG C 628 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ILE cc_start: 0.9446 (mm) cc_final: 0.8981 (tp) REVERT: A 140 ASP cc_start: 0.8293 (m-30) cc_final: 0.7986 (t0) REVERT: A 195 ASP cc_start: 0.8594 (t0) cc_final: 0.8276 (t0) REVERT: A 214 HIS cc_start: 0.9031 (p-80) cc_final: 0.8827 (p90) REVERT: A 463 MET cc_start: 0.8957 (mmm) cc_final: 0.8292 (mmt) REVERT: A 527 MET cc_start: 0.7261 (mmp) cc_final: 0.6684 (mmm) REVERT: A 540 LEU cc_start: 0.8992 (tp) cc_final: 0.8705 (tp) REVERT: A 661 ARG cc_start: 0.9059 (mmt180) cc_final: 0.8536 (ttp80) REVERT: A 674 MET cc_start: 0.9328 (ptp) cc_final: 0.9093 (ptt) REVERT: A 798 ILE cc_start: 0.9396 (mt) cc_final: 0.8999 (tt) REVERT: B 25 GLU cc_start: 0.8972 (mp0) cc_final: 0.8654 (mp0) REVERT: B 93 HIS cc_start: 0.8733 (m90) cc_final: 0.8512 (m-70) REVERT: B 113 MET cc_start: 0.9116 (mpp) cc_final: 0.8881 (mpp) REVERT: B 175 GLU cc_start: 0.9543 (mp0) cc_final: 0.9177 (pm20) REVERT: B 292 MET cc_start: 0.8043 (ppp) cc_final: 0.7662 (ppp) REVERT: B 378 ASP cc_start: 0.9129 (m-30) cc_final: 0.8845 (m-30) REVERT: B 517 PHE cc_start: 0.8202 (p90) cc_final: 0.7984 (p90) REVERT: B 533 TYR cc_start: 0.8582 (t80) cc_final: 0.7871 (t80) REVERT: B 538 VAL cc_start: 0.9393 (p) cc_final: 0.9192 (p) REVERT: B 612 ILE cc_start: 0.9435 (mm) cc_final: 0.9019 (tt) REVERT: B 708 MET cc_start: 0.9047 (ttp) cc_final: 0.8657 (ptm) REVERT: B 709 ASN cc_start: 0.8245 (t0) cc_final: 0.7989 (t0) REVERT: B 798 ILE cc_start: 0.8778 (mt) cc_final: 0.8335 (tt) REVERT: C 33 MET cc_start: 0.9373 (ttt) cc_final: 0.8737 (tmm) REVERT: C 88 PHE cc_start: 0.8506 (m-10) cc_final: 0.8063 (m-80) REVERT: C 292 MET cc_start: 0.9287 (ppp) cc_final: 0.9043 (ppp) REVERT: C 442 LEU cc_start: 0.9267 (mt) cc_final: 0.9033 (mt) REVERT: C 585 MET cc_start: 0.9082 (mmt) cc_final: 0.8879 (mmm) REVERT: D 33 MET cc_start: 0.8875 (ppp) cc_final: 0.8623 (ppp) REVERT: D 83 ASN cc_start: 0.9106 (p0) cc_final: 0.8553 (p0) REVERT: D 93 HIS cc_start: 0.8976 (m-70) cc_final: 0.8561 (m-70) REVERT: D 113 MET cc_start: 0.8647 (tpt) cc_final: 0.6920 (tpp) REVERT: D 193 ILE cc_start: 0.9246 (mp) cc_final: 0.8957 (mm) REVERT: D 231 ASP cc_start: 0.8620 (t0) cc_final: 0.8299 (t0) REVERT: D 284 LEU cc_start: 0.9315 (mm) cc_final: 0.8192 (mm) REVERT: D 361 MET cc_start: 0.6612 (mmm) cc_final: 0.6211 (mmm) REVERT: D 378 ASP cc_start: 0.8832 (m-30) cc_final: 0.7963 (m-30) REVERT: D 463 MET cc_start: 0.5700 (mmp) cc_final: 0.5228 (mmm) REVERT: D 527 MET cc_start: 0.7906 (mtp) cc_final: 0.7428 (mtp) REVERT: D 612 ILE cc_start: 0.9544 (mm) cc_final: 0.9247 (tt) REVERT: D 795 VAL cc_start: 0.8412 (p) cc_final: 0.8202 (m) REVERT: D 798 ILE cc_start: 0.8695 (mt) cc_final: 0.8212 (tt) outliers start: 1 outliers final: 0 residues processed: 338 average time/residue: 0.3165 time to fit residues: 176.0236 Evaluate side-chains 257 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 294 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 223 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 304 optimal weight: 20.0000 chunk 190 optimal weight: 0.0870 chunk 185 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 overall best weight: 1.3962 ------------------------------------------------------------------------------- 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: 0.7504 moved from start: 0.7004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25710 Z= 0.172 Angle : 0.559 11.786 34738 Z= 0.290 Chirality : 0.042 0.201 3830 Planarity : 0.004 0.063 4395 Dihedral : 4.498 64.230 3519 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.92 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.15), residues: 3164 helix: 1.38 (0.14), residues: 1480 sheet: -0.74 (0.26), residues: 397 loop : -0.37 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 526 HIS 0.005 0.001 HIS A 214 PHE 0.017 0.001 PHE D 517 TYR 0.017 0.001 TYR A 286 ARG 0.004 0.000 ARG D 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ILE cc_start: 0.9440 (mm) cc_final: 0.8965 (tp) REVERT: A 140 ASP cc_start: 0.8395 (m-30) cc_final: 0.7956 (t0) REVERT: A 214 HIS cc_start: 0.9015 (p-80) cc_final: 0.8686 (p-80) REVERT: A 356 TYR cc_start: 0.8960 (p90) cc_final: 0.8667 (p90) REVERT: A 399 THR cc_start: 0.9202 (p) cc_final: 0.8995 (p) REVERT: A 463 MET cc_start: 0.8947 (mmm) cc_final: 0.8336 (mmt) REVERT: A 527 MET cc_start: 0.7216 (mmp) cc_final: 0.6373 (mmm) REVERT: A 540 LEU cc_start: 0.8868 (tp) cc_final: 0.8547 (tp) REVERT: A 541 PHE cc_start: 0.7751 (t80) cc_final: 0.7382 (t80) REVERT: A 661 ARG cc_start: 0.9037 (mmt180) cc_final: 0.8517 (ttp80) REVERT: A 674 MET cc_start: 0.9315 (ptp) cc_final: 0.9108 (ptt) REVERT: A 798 ILE cc_start: 0.9373 (mt) cc_final: 0.8916 (tt) REVERT: B 17 LEU cc_start: 0.8887 (tp) cc_final: 0.8561 (mm) REVERT: B 25 GLU cc_start: 0.8965 (mp0) cc_final: 0.8635 (mp0) REVERT: B 113 MET cc_start: 0.9173 (mpp) cc_final: 0.8838 (mpp) REVERT: B 175 GLU cc_start: 0.9550 (mp0) cc_final: 0.9154 (pm20) REVERT: B 292 MET cc_start: 0.8051 (ppp) cc_final: 0.7677 (ppp) REVERT: B 378 ASP cc_start: 0.9076 (m-30) cc_final: 0.8826 (m-30) REVERT: B 517 PHE cc_start: 0.8063 (p90) cc_final: 0.7700 (p90) REVERT: B 612 ILE cc_start: 0.9415 (mm) cc_final: 0.9116 (tt) REVERT: B 614 SER cc_start: 0.9168 (p) cc_final: 0.8638 (t) REVERT: B 708 MET cc_start: 0.9017 (ttp) cc_final: 0.8600 (ptm) REVERT: B 798 ILE cc_start: 0.8516 (mt) cc_final: 0.8171 (tt) REVERT: C 88 PHE cc_start: 0.8496 (m-10) cc_final: 0.8067 (m-80) REVERT: C 113 MET cc_start: 0.8962 (mmp) cc_final: 0.8615 (mmp) REVERT: C 292 MET cc_start: 0.9284 (ppp) cc_final: 0.9049 (ppp) REVERT: C 361 MET cc_start: 0.7299 (mpp) cc_final: 0.7030 (mpp) REVERT: C 442 LEU cc_start: 0.9265 (mt) cc_final: 0.9043 (mt) REVERT: C 527 MET cc_start: 0.7369 (mmp) cc_final: 0.6378 (mmm) REVERT: C 540 LEU cc_start: 0.8812 (tp) cc_final: 0.8518 (tp) REVERT: C 670 MET cc_start: 0.9049 (ptp) cc_final: 0.8617 (ptp) REVERT: C 798 ILE cc_start: 0.9186 (mm) cc_final: 0.8929 (tt) REVERT: C 805 LEU cc_start: 0.9103 (tt) cc_final: 0.8868 (mm) REVERT: D 83 ASN cc_start: 0.9137 (p0) cc_final: 0.8633 (p0) REVERT: D 93 HIS cc_start: 0.8941 (m-70) cc_final: 0.8546 (m-70) REVERT: D 113 MET cc_start: 0.8646 (tpt) cc_final: 0.6937 (tpp) REVERT: D 159 GLN cc_start: 0.8903 (tm-30) cc_final: 0.8652 (tm-30) REVERT: D 193 ILE cc_start: 0.9194 (mp) cc_final: 0.8905 (mm) REVERT: D 231 ASP cc_start: 0.8591 (t0) cc_final: 0.8178 (t0) REVERT: D 284 LEU cc_start: 0.9333 (mm) cc_final: 0.8085 (mm) REVERT: D 463 MET cc_start: 0.5595 (mmp) cc_final: 0.5110 (mmm) REVERT: D 518 LEU cc_start: 0.8713 (mp) cc_final: 0.8312 (mt) REVERT: D 527 MET cc_start: 0.7904 (mtp) cc_final: 0.7438 (mtp) REVERT: D 541 PHE cc_start: 0.8181 (t80) cc_final: 0.7768 (t80) REVERT: D 573 ILE cc_start: 0.8718 (tp) cc_final: 0.8174 (tt) REVERT: D 612 ILE cc_start: 0.9517 (mm) cc_final: 0.9210 (tt) REVERT: D 614 SER cc_start: 0.9276 (p) cc_final: 0.8902 (t) REVERT: D 798 ILE cc_start: 0.8852 (mt) cc_final: 0.8164 (tt) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.3403 time to fit residues: 197.7489 Evaluate side-chains 268 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 188 optimal weight: 0.0070 chunk 121 optimal weight: 20.0000 chunk 181 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 239 optimal weight: 8.9990 chunk 277 optimal weight: 20.0000 overall best weight: 5.2006 ------------------------------------------------------------------------------- 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: 0.7655 moved from start: 0.7945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 25710 Z= 0.405 Angle : 0.753 12.991 34738 Z= 0.397 Chirality : 0.046 0.201 3830 Planarity : 0.005 0.079 4395 Dihedral : 5.321 62.018 3519 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.53 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.12 (0.15), residues: 3164 helix: 0.74 (0.13), residues: 1480 sheet: -1.02 (0.27), residues: 369 loop : -0.63 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP C 526 HIS 0.012 0.002 HIS A 214 PHE 0.031 0.003 PHE C 541 TYR 0.021 0.002 TYR D 127 ARG 0.007 0.001 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LYS cc_start: 0.9270 (mtmm) cc_final: 0.9039 (mttp) REVERT: A 140 ASP cc_start: 0.8364 (m-30) cc_final: 0.8164 (t0) REVERT: A 463 MET cc_start: 0.8895 (mmm) cc_final: 0.8579 (mmm) REVERT: A 527 MET cc_start: 0.7265 (mmp) cc_final: 0.6794 (mmm) REVERT: A 540 LEU cc_start: 0.9008 (tp) cc_final: 0.8786 (tp) REVERT: A 661 ARG cc_start: 0.9055 (mmt180) cc_final: 0.8553 (ttp80) REVERT: A 789 LEU cc_start: 0.8585 (tp) cc_final: 0.8289 (tp) REVERT: B 175 GLU cc_start: 0.9570 (mp0) cc_final: 0.9283 (mp0) REVERT: B 292 MET cc_start: 0.8068 (ppp) cc_final: 0.7846 (ppp) REVERT: B 316 LEU cc_start: 0.8185 (mt) cc_final: 0.7698 (pp) REVERT: B 378 ASP cc_start: 0.9149 (m-30) cc_final: 0.8881 (m-30) REVERT: B 709 ASN cc_start: 0.8346 (t0) cc_final: 0.7950 (t0) REVERT: C 113 MET cc_start: 0.9177 (mmp) cc_final: 0.8913 (mmp) REVERT: C 160 VAL cc_start: 0.9600 (t) cc_final: 0.9372 (m) REVERT: C 292 MET cc_start: 0.9238 (ppp) cc_final: 0.9017 (ppp) REVERT: C 442 LEU cc_start: 0.9345 (mt) cc_final: 0.9077 (mt) REVERT: C 527 MET cc_start: 0.7637 (mmp) cc_final: 0.7042 (mmm) REVERT: C 540 LEU cc_start: 0.8896 (tp) cc_final: 0.8662 (tp) REVERT: D 17 LEU cc_start: 0.9574 (mt) cc_final: 0.9372 (mt) REVERT: D 33 MET cc_start: 0.8857 (ppp) cc_final: 0.8545 (ppp) REVERT: D 83 ASN cc_start: 0.9152 (p0) cc_final: 0.8770 (p0) REVERT: D 113 MET cc_start: 0.8650 (tpt) cc_final: 0.7727 (tpp) REVERT: D 193 ILE cc_start: 0.9213 (mp) cc_final: 0.8979 (mm) REVERT: D 463 MET cc_start: 0.5999 (mmp) cc_final: 0.5551 (mmm) REVERT: D 527 MET cc_start: 0.7925 (mtp) cc_final: 0.7540 (mtp) REVERT: D 533 TYR cc_start: 0.8285 (t80) cc_final: 0.7569 (t80) REVERT: D 798 ILE cc_start: 0.8909 (mt) cc_final: 0.8330 (tt) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.3265 time to fit residues: 160.8289 Evaluate side-chains 224 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 2.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 291 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 283 optimal weight: 30.0000 chunk 170 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 222 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 256 optimal weight: 0.8980 chunk 268 optimal weight: 9.9990 chunk 282 optimal weight: 8.9990 chunk 186 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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: 0.7568 moved from start: 0.7960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25710 Z= 0.203 Angle : 0.606 12.153 34738 Z= 0.314 Chirality : 0.043 0.187 3830 Planarity : 0.004 0.066 4395 Dihedral : 4.847 64.920 3519 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.27 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.22 (0.15), residues: 3164 helix: 1.10 (0.14), residues: 1476 sheet: -1.00 (0.27), residues: 387 loop : -0.50 (0.18), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 526 HIS 0.006 0.001 HIS A 214 PHE 0.017 0.001 PHE A 88 TYR 0.017 0.001 TYR A 77 ARG 0.006 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LYS cc_start: 0.9221 (mtmm) cc_final: 0.9004 (mttp) REVERT: A 129 GLN cc_start: 0.9092 (tm-30) cc_final: 0.8753 (tm-30) REVERT: A 140 ASP cc_start: 0.8301 (m-30) cc_final: 0.7999 (t0) REVERT: A 334 LYS cc_start: 0.9481 (mtmt) cc_final: 0.9076 (mttt) REVERT: A 356 TYR cc_start: 0.8963 (p90) cc_final: 0.8679 (p90) REVERT: A 442 LEU cc_start: 0.9159 (mt) cc_final: 0.8951 (mt) REVERT: A 463 MET cc_start: 0.8962 (mmm) cc_final: 0.8671 (mmm) REVERT: A 527 MET cc_start: 0.7314 (mmp) cc_final: 0.6793 (mmm) REVERT: A 661 ARG cc_start: 0.8993 (mmt180) cc_final: 0.8470 (ttp80) REVERT: A 666 VAL cc_start: 0.9232 (m) cc_final: 0.8831 (p) REVERT: A 670 MET cc_start: 0.8976 (ptp) cc_final: 0.8569 (ptp) REVERT: A 798 ILE cc_start: 0.9364 (mt) cc_final: 0.8870 (tt) REVERT: B 113 MET cc_start: 0.9117 (mpp) cc_final: 0.8900 (mpp) REVERT: B 175 GLU cc_start: 0.9584 (mp0) cc_final: 0.9128 (pm20) REVERT: B 292 MET cc_start: 0.8095 (ppp) cc_final: 0.7799 (ppp) REVERT: B 316 LEU cc_start: 0.8095 (mt) cc_final: 0.7711 (pp) REVERT: B 378 ASP cc_start: 0.9156 (m-30) cc_final: 0.8890 (m-30) REVERT: B 517 PHE cc_start: 0.7944 (p90) cc_final: 0.7486 (p90) REVERT: B 518 LEU cc_start: 0.9095 (mt) cc_final: 0.8792 (mt) REVERT: B 581 LEU cc_start: 0.8802 (tt) cc_final: 0.8541 (tt) REVERT: B 612 ILE cc_start: 0.9448 (mm) cc_final: 0.9104 (tt) REVERT: B 709 ASN cc_start: 0.8250 (t0) cc_final: 0.7805 (t0) REVERT: B 798 ILE cc_start: 0.8568 (mt) cc_final: 0.8055 (tt) REVERT: C 113 MET cc_start: 0.9169 (mmp) cc_final: 0.8868 (mmp) REVERT: C 160 VAL cc_start: 0.9561 (t) cc_final: 0.9322 (m) REVERT: C 292 MET cc_start: 0.9320 (ppp) cc_final: 0.9018 (ppp) REVERT: C 361 MET cc_start: 0.6907 (mpp) cc_final: 0.6579 (mpp) REVERT: C 442 LEU cc_start: 0.9346 (mt) cc_final: 0.9118 (mt) REVERT: C 527 MET cc_start: 0.7534 (mmp) cc_final: 0.6835 (mmm) REVERT: C 540 LEU cc_start: 0.8790 (tp) cc_final: 0.8555 (tp) REVERT: C 798 ILE cc_start: 0.9434 (mt) cc_final: 0.8948 (tt) REVERT: D 83 ASN cc_start: 0.9157 (p0) cc_final: 0.8703 (p0) REVERT: D 113 MET cc_start: 0.8759 (tpt) cc_final: 0.7549 (tpp) REVERT: D 141 ARG cc_start: 0.8517 (mmt90) cc_final: 0.8239 (tpp80) REVERT: D 193 ILE cc_start: 0.9188 (mp) cc_final: 0.8895 (mm) REVERT: D 463 MET cc_start: 0.5535 (mmp) cc_final: 0.5143 (mmm) REVERT: D 518 LEU cc_start: 0.8745 (mp) cc_final: 0.8456 (mt) REVERT: D 527 MET cc_start: 0.7915 (mtp) cc_final: 0.7456 (mtp) REVERT: D 612 ILE cc_start: 0.9569 (mm) cc_final: 0.9253 (tt) REVERT: D 795 VAL cc_start: 0.8201 (p) cc_final: 0.7956 (m) REVERT: D 798 ILE cc_start: 0.8633 (mt) cc_final: 0.7940 (tt) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.3429 time to fit residues: 189.0812 Evaluate side-chains 243 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 300 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 142 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 314 optimal weight: 6.9990 chunk 289 optimal weight: 2.9990 chunk 250 optimal weight: 6.9990 chunk 26 optimal weight: 0.0370 chunk 193 optimal weight: 0.2980 chunk 153 optimal weight: 9.9990 chunk 199 optimal weight: 1.9990 overall best weight: 1.2662 ------------------------------------------------------------------------------- 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: 0.7542 moved from start: 0.8065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25710 Z= 0.175 Angle : 0.593 12.556 34738 Z= 0.305 Chirality : 0.043 0.198 3830 Planarity : 0.004 0.061 4395 Dihedral : 4.594 64.087 3519 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.42 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3164 helix: 1.21 (0.14), residues: 1489 sheet: -0.88 (0.27), residues: 393 loop : -0.47 (0.18), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 578 HIS 0.005 0.001 HIS A 214 PHE 0.017 0.001 PHE A 531 TYR 0.015 0.001 TYR A 286 ARG 0.006 0.000 ARG A 599 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6328 Ramachandran restraints generated. 3164 Oldfield, 0 Emsley, 3164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.9491 (pt) cc_final: 0.8960 (tp) REVERT: A 118 LYS cc_start: 0.9213 (mtmm) cc_final: 0.8941 (mttp) REVERT: A 129 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8704 (tm-30) REVERT: A 140 ASP cc_start: 0.8307 (m-30) cc_final: 0.7864 (t0) REVERT: A 334 LYS cc_start: 0.9481 (mtmt) cc_final: 0.9053 (mttt) REVERT: A 356 TYR cc_start: 0.8942 (p90) cc_final: 0.8649 (p90) REVERT: A 442 LEU cc_start: 0.9133 (mt) cc_final: 0.8918 (mt) REVERT: A 527 MET cc_start: 0.7301 (mmp) cc_final: 0.6660 (mmm) REVERT: A 540 LEU cc_start: 0.8784 (tp) cc_final: 0.8552 (tp) REVERT: A 661 ARG cc_start: 0.8993 (mmt180) cc_final: 0.8459 (ttp80) REVERT: A 798 ILE cc_start: 0.9330 (mt) cc_final: 0.8853 (tt) REVERT: B 113 MET cc_start: 0.9114 (mpp) cc_final: 0.8897 (mpp) REVERT: B 138 ASP cc_start: 0.8069 (t0) cc_final: 0.7564 (t70) REVERT: B 175 GLU cc_start: 0.9559 (mp0) cc_final: 0.9178 (pm20) REVERT: B 292 MET cc_start: 0.8065 (ppp) cc_final: 0.7792 (ppp) REVERT: B 316 LEU cc_start: 0.7970 (mt) cc_final: 0.7689 (pp) REVERT: B 378 ASP cc_start: 0.9162 (m-30) cc_final: 0.8897 (m-30) REVERT: B 517 PHE cc_start: 0.7872 (p90) cc_final: 0.7533 (p90) REVERT: B 612 ILE cc_start: 0.9472 (mm) cc_final: 0.9075 (tt) REVERT: B 614 SER cc_start: 0.9182 (p) cc_final: 0.8723 (t) REVERT: B 638 ASP cc_start: 0.9037 (m-30) cc_final: 0.8810 (m-30) REVERT: B 798 ILE cc_start: 0.8552 (mt) cc_final: 0.8062 (tt) REVERT: C 113 MET cc_start: 0.9160 (mmp) cc_final: 0.8809 (mmp) REVERT: C 361 MET cc_start: 0.7078 (mpp) cc_final: 0.6793 (mpp) REVERT: C 442 LEU cc_start: 0.9317 (mt) cc_final: 0.9081 (mt) REVERT: C 479 LEU cc_start: 0.8985 (pp) cc_final: 0.8712 (mm) REVERT: C 527 MET cc_start: 0.7403 (mmp) cc_final: 0.6516 (mmm) REVERT: C 540 LEU cc_start: 0.8729 (tp) cc_final: 0.8454 (tp) REVERT: C 585 MET cc_start: 0.9032 (mmt) cc_final: 0.8830 (mmp) REVERT: C 789 LEU cc_start: 0.7430 (mm) cc_final: 0.7116 (pt) REVERT: C 798 ILE cc_start: 0.9407 (mt) cc_final: 0.8870 (tt) REVERT: D 83 ASN cc_start: 0.9140 (p0) cc_final: 0.8699 (p0) REVERT: D 113 MET cc_start: 0.8762 (tpt) cc_final: 0.7675 (tpp) REVERT: D 141 ARG cc_start: 0.8562 (mmt90) cc_final: 0.8313 (tpp80) REVERT: D 193 ILE cc_start: 0.9210 (mp) cc_final: 0.8933 (mm) REVERT: D 231 ASP cc_start: 0.8877 (t0) cc_final: 0.8647 (t0) REVERT: D 284 LEU cc_start: 0.9471 (mm) cc_final: 0.8616 (mm) REVERT: D 361 MET cc_start: 0.6868 (mmm) cc_final: 0.6282 (mmm) REVERT: D 380 MET cc_start: 0.7897 (tmm) cc_final: 0.7247 (tmm) REVERT: D 463 MET cc_start: 0.5462 (mmp) cc_final: 0.5055 (mmm) REVERT: D 518 LEU cc_start: 0.8756 (mp) cc_final: 0.8317 (mt) REVERT: D 527 MET cc_start: 0.7972 (mtp) cc_final: 0.7403 (ttm) REVERT: D 540 LEU cc_start: 0.8754 (tp) cc_final: 0.8417 (tp) REVERT: D 612 ILE cc_start: 0.9561 (mm) cc_final: 0.9247 (tt) REVERT: D 795 VAL cc_start: 0.8088 (p) cc_final: 0.7780 (m) REVERT: D 798 ILE cc_start: 0.8590 (mt) cc_final: 0.7913 (tt) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.3482 time to fit residues: 189.6684 Evaluate side-chains 249 residues out of total 2720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 267 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 231 optimal weight: 0.9990 chunk 37 optimal weight: 0.0870 chunk 69 optimal weight: 0.9980 chunk 251 optimal weight: 0.5980 chunk 105 optimal weight: 6.9990 chunk 257 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 220 optimal weight: 0.3980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.3306 r_free = 0.3306 target = 0.058919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.040945 restraints weight = 149918.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.042321 restraints weight = 99548.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.043274 restraints weight = 75281.527| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.8115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25710 Z= 0.156 Angle : 0.591 12.334 34738 Z= 0.302 Chirality : 0.043 0.221 3830 Planarity : 0.004 0.078 4395 Dihedral : 4.420 65.319 3519 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.01 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.39 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.16), residues: 3164 helix: 1.29 (0.14), residues: 1475 sheet: -0.74 (0.27), residues: 389 loop : -0.37 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 578 HIS 0.007 0.001 HIS B 219 PHE 0.020 0.001 PHE A 88 TYR 0.016 0.001 TYR A 286 ARG 0.004 0.000 ARG A 141 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 5125.43 seconds wall clock time: 91 minutes 42.52 seconds (5502.52 seconds total)