Starting phenix.real_space_refine on Thu Sep 26 20:44:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ain_11799/09_2024/7ain_11799.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ain_11799/09_2024/7ain_11799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ain_11799/09_2024/7ain_11799.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ain_11799/09_2024/7ain_11799.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ain_11799/09_2024/7ain_11799.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ain_11799/09_2024/7ain_11799.cif" } resolution = 3.2 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= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 94 5.16 5 C 9020 2.51 5 N 2300 2.21 5 O 2486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13904 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 6899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 6899 Classifications: {'peptide': 904} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 34, 'TRANS': 869} Chain breaks: 3 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TPO:plan-1': 1, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 6899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 6899 Classifications: {'peptide': 904} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 34, 'TRANS': 869} Chain breaks: 3 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TPO:plan-1': 1, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.60, per 1000 atoms: 0.69 Number of scatterers: 13904 At special positions: 0 Unit cell: (104.811, 92.442, 147.126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 94 16.00 P 4 15.00 O 2486 8.00 N 2300 7.00 C 9020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 640 " distance=2.04 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 359 " - pdb=" SG CYS B 369 " distance=2.02 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 640 " distance=2.04 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 359 " - pdb=" SG CYS A 369 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A1101 " - " ASN A 377 " " NAG B1101 " - " ASN B 377 " " NAG C 1 " - " ASN B 328 " " NAG G 1 " - " ASN A 328 " Time building additional restraints: 3.79 Conformation dependent library (CDL) restraints added in 1.7 seconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3332 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 8 sheets defined 61.5% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'B' and resid 111 through 122 Processing helix chain 'B' and resid 127 through 131 removed outlier: 3.676A pdb=" N THR B 131 " --> pdb=" O LYS B 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 127 through 131' Processing helix chain 'B' and resid 135 through 149 removed outlier: 5.151A pdb=" N LEU B 142 " --> pdb=" O MET B 138 " (cutoff:3.500A) Proline residue: B 143 - end of helix Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 156 through 193 removed outlier: 6.234A pdb=" N VAL B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N LEU B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 243 removed outlier: 3.529A pdb=" N MET B 204 " --> pdb=" O GLY B 200 " (cutoff:3.500A) Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 258 through 284 Processing helix chain 'B' and resid 285 through 314 removed outlier: 3.662A pdb=" N VAL B 289 " --> pdb=" O GLY B 285 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N SER B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 359 Processing helix chain 'B' and resid 370 through 376 Processing helix chain 'B' and resid 390 through 394 removed outlier: 3.502A pdb=" N THR B 393 " --> pdb=" O GLY B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 removed outlier: 3.695A pdb=" N GLY B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 445 No H-bonds generated for 'chain 'B' and resid 443 through 445' Processing helix chain 'B' and resid 447 through 453 Processing helix chain 'B' and resid 460 through 491 Proline residue: B 466 - end of helix removed outlier: 3.672A pdb=" N VAL B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 517 through 550 removed outlier: 4.256A pdb=" N ILE B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Proline residue: B 541 - end of helix Processing helix chain 'B' and resid 554 through 561 removed outlier: 3.920A pdb=" N VAL B 558 " --> pdb=" O PHE B 555 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS B 561 " --> pdb=" O VAL B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 584 removed outlier: 3.691A pdb=" N LEU B 572 " --> pdb=" O PRO B 568 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 616 Proline residue: B 593 - end of helix removed outlier: 3.659A pdb=" N CYS B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 648 removed outlier: 3.606A pdb=" N SER B 633 " --> pdb=" O HIS B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 675 removed outlier: 3.603A pdb=" N ILE B 653 " --> pdb=" O TRP B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 696 removed outlier: 3.599A pdb=" N GLU B 696 " --> pdb=" O LEU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 734 removed outlier: 4.289A pdb=" N LEU B 726 " --> pdb=" O HIS B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 770 Processing helix chain 'B' and resid 783 through 795 removed outlier: 3.938A pdb=" N GLN B 793 " --> pdb=" O SER B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 835 removed outlier: 3.545A pdb=" N PHE B 825 " --> pdb=" O ALA B 821 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 826 " --> pdb=" O TRP B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 Processing helix chain 'B' and resid 868 through 881 removed outlier: 3.640A pdb=" N LEU B 872 " --> pdb=" O ASP B 868 " (cutoff:3.500A) Proline residue: B 876 - end of helix Processing helix chain 'B' and resid 904 through 917 Processing helix chain 'B' and resid 932 through 946 Processing helix chain 'B' and resid 1029 through 1048 removed outlier: 3.914A pdb=" N LYS B1038 " --> pdb=" O HIS B1034 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1065 No H-bonds generated for 'chain 'B' and resid 1063 through 1065' Processing helix chain 'B' and resid 1066 through 1078 Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.676A pdb=" N THR A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 127 through 131' Processing helix chain 'A' and resid 135 through 149 removed outlier: 5.151A pdb=" N LEU A 142 " --> pdb=" O MET A 138 " (cutoff:3.500A) Proline residue: A 143 - end of helix Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 156 through 193 removed outlier: 6.234A pdb=" N VAL A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N LEU A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 243 removed outlier: 3.530A pdb=" N MET A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 211 - end of helix Processing helix chain 'A' and resid 258 through 284 Processing helix chain 'A' and resid 285 through 314 removed outlier: 3.661A pdb=" N VAL A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N SER A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LEU A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 Processing helix chain 'A' and resid 370 through 376 Processing helix chain 'A' and resid 390 through 394 removed outlier: 3.502A pdb=" N THR A 393 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 removed outlier: 3.696A pdb=" N GLY A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 447 through 453 Processing helix chain 'A' and resid 460 through 491 Proline residue: A 466 - end of helix removed outlier: 3.673A pdb=" N VAL A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 517 through 550 removed outlier: 4.257A pdb=" N ILE A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Proline residue: A 541 - end of helix Processing helix chain 'A' and resid 554 through 561 removed outlier: 3.919A pdb=" N VAL A 558 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS A 561 " --> pdb=" O VAL A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 584 removed outlier: 3.691A pdb=" N LEU A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 616 Proline residue: A 593 - end of helix removed outlier: 3.659A pdb=" N CYS A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 648 removed outlier: 3.606A pdb=" N SER A 633 " --> pdb=" O HIS A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 675 removed outlier: 3.604A pdb=" N ILE A 653 " --> pdb=" O TRP A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 696 removed outlier: 3.599A pdb=" N GLU A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 734 removed outlier: 4.289A pdb=" N LEU A 726 " --> pdb=" O HIS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 770 Processing helix chain 'A' and resid 783 through 795 removed outlier: 3.938A pdb=" N GLN A 793 " --> pdb=" O SER A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 835 removed outlier: 3.545A pdb=" N PHE A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 826 " --> pdb=" O TRP A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'A' and resid 868 through 881 removed outlier: 3.640A pdb=" N LEU A 872 " --> pdb=" O ASP A 868 " (cutoff:3.500A) Proline residue: A 876 - end of helix Processing helix chain 'A' and resid 904 through 917 Processing helix chain 'A' and resid 932 through 946 Processing helix chain 'A' and resid 1029 through 1048 removed outlier: 3.914A pdb=" N LYS A1038 " --> pdb=" O HIS A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1066 through 1078 Processing sheet with id=AA1, first strand: chain 'B' and resid 329 through 330 Processing sheet with id=AA2, first strand: chain 'B' and resid 342 through 345 removed outlier: 3.574A pdb=" N VAL B 350 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 775 through 781 removed outlier: 6.675A pdb=" N LEU B 708 " --> pdb=" O ILE B 740 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLY B 742 " --> pdb=" O LEU B 708 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL B 710 " --> pdb=" O GLY B 742 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL B 744 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY B 808 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL B 805 " --> pdb=" O LEU B 840 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA B 842 " --> pdb=" O VAL B 805 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N MET B 807 " --> pdb=" O ALA B 842 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B1084 " --> pdb=" O LYS B 843 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B1053 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL B1087 " --> pdb=" O VAL B1053 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU B1055 " --> pdb=" O VAL B1087 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 859 through 860 removed outlier: 6.785A pdb=" N ILE B 890 " --> pdb=" O GLU B 921 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N GLU B 923 " --> pdb=" O ILE B 890 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE B 892 " --> pdb=" O GLU B 923 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA6, first strand: chain 'A' and resid 342 through 345 removed outlier: 3.575A pdb=" N VAL A 350 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 775 through 781 removed outlier: 6.674A pdb=" N LEU A 708 " --> pdb=" O ILE A 740 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLY A 742 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL A 710 " --> pdb=" O GLY A 742 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL A 744 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY A 808 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL A 805 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA A 842 " --> pdb=" O VAL A 805 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N MET A 807 " --> pdb=" O ALA A 842 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A1084 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A1053 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL A1087 " --> pdb=" O VAL A1053 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU A1055 " --> pdb=" O VAL A1087 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 859 through 860 removed outlier: 6.784A pdb=" N ILE A 890 " --> pdb=" O GLU A 921 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N GLU A 923 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE A 892 " --> pdb=" O GLU A 923 " (cutoff:3.500A) 812 hydrogen bonds defined for protein. 2346 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: 4.68 Time building geometry restraints manager: 4.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4376 1.35 - 1.47: 3663 1.47 - 1.60: 6015 1.60 - 1.73: 14 1.73 - 1.86: 150 Bond restraints: 14218 Sorted by residual: bond pdb=" OG1 TPO B 727 " pdb=" P TPO B 727 " ideal model delta sigma weight residual 1.717 1.617 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" OG1 TPO A 727 " pdb=" P TPO A 727 " ideal model delta sigma weight residual 1.717 1.617 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" O1P TPO A 727 " pdb=" P TPO A 727 " ideal model delta sigma weight residual 1.525 1.614 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" O1P TPO B 727 " pdb=" P TPO B 727 " ideal model delta sigma weight residual 1.525 1.614 -0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" O2P TPO A 727 " pdb=" P TPO A 727 " ideal model delta sigma weight residual 1.528 1.605 -0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 14213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 18738 2.34 - 4.67: 526 4.67 - 7.01: 63 7.01 - 9.35: 13 9.35 - 11.69: 2 Bond angle restraints: 19342 Sorted by residual: angle pdb=" C VAL B 866 " pdb=" N HIS B 867 " pdb=" CA HIS B 867 " ideal model delta sigma weight residual 122.53 115.85 6.68 1.61e+00 3.86e-01 1.72e+01 angle pdb=" C VAL A 866 " pdb=" N HIS A 867 " pdb=" CA HIS A 867 " ideal model delta sigma weight residual 122.53 115.88 6.65 1.61e+00 3.86e-01 1.71e+01 angle pdb=" CA CYS B 640 " pdb=" CB CYS B 640 " pdb=" SG CYS B 640 " ideal model delta sigma weight residual 114.40 122.59 -8.19 2.30e+00 1.89e-01 1.27e+01 angle pdb=" CA CYS A 640 " pdb=" CB CYS A 640 " pdb=" SG CYS A 640 " ideal model delta sigma weight residual 114.40 122.58 -8.18 2.30e+00 1.89e-01 1.27e+01 angle pdb=" C ASP A 255 " pdb=" CA ASP A 255 " pdb=" CB ASP A 255 " ideal model delta sigma weight residual 116.63 112.53 4.10 1.16e+00 7.43e-01 1.25e+01 ... (remaining 19337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.88: 7986 20.88 - 41.76: 354 41.76 - 62.64: 68 62.64 - 83.52: 22 83.52 - 104.39: 8 Dihedral angle restraints: 8438 sinusoidal: 3256 harmonic: 5182 Sorted by residual: dihedral pdb=" CA CYS B 640 " pdb=" C CYS B 640 " pdb=" N LEU B 641 " pdb=" CA LEU B 641 " ideal model delta harmonic sigma weight residual 180.00 155.75 24.25 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA CYS A 640 " pdb=" C CYS A 640 " pdb=" N LEU A 641 " pdb=" CA LEU A 641 " ideal model delta harmonic sigma weight residual 180.00 155.76 24.24 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CB CYS A 179 " pdb=" SG CYS A 179 " pdb=" SG CYS A 640 " pdb=" CB CYS A 640 " ideal model delta sinusoidal sigma weight residual 93.00 60.81 32.19 1 1.00e+01 1.00e-02 1.48e+01 ... (remaining 8435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1924 0.079 - 0.157: 345 0.157 - 0.236: 15 0.236 - 0.314: 2 0.314 - 0.393: 2 Chirality restraints: 2288 Sorted by residual: chirality pdb=" CA CYS B 640 " pdb=" N CYS B 640 " pdb=" C CYS B 640 " pdb=" CB CYS B 640 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CA CYS A 640 " pdb=" N CYS A 640 " pdb=" C CYS A 640 " pdb=" CB CYS A 640 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 2285 not shown) Planarity restraints: 2404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 497 " -0.094 9.50e-02 1.11e+02 5.58e-02 1.77e+01 pdb=" NE ARG B 497 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 497 " -0.069 2.00e-02 2.50e+03 pdb=" NH1 ARG B 497 " 0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG B 497 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 497 " 0.093 9.50e-02 1.11e+02 5.54e-02 1.76e+01 pdb=" NE ARG A 497 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 497 " 0.069 2.00e-02 2.50e+03 pdb=" NH1 ARG A 497 " -0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG A 497 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 240 " 0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C PHE A 240 " -0.070 2.00e-02 2.50e+03 pdb=" O PHE A 240 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU A 241 " 0.024 2.00e-02 2.50e+03 ... (remaining 2401 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 4005 2.81 - 3.33: 14280 3.33 - 3.85: 23380 3.85 - 4.38: 27096 4.38 - 4.90: 46636 Nonbonded interactions: 115397 Sorted by model distance: nonbonded pdb=" OH TYR B 141 " pdb=" OG1 THR B 475 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR A 141 " pdb=" OG1 THR A 475 " model vdw 2.282 3.040 nonbonded pdb=" O SER B1092 " pdb=" OG SER B1092 " model vdw 2.291 3.040 nonbonded pdb=" ND2 ASN B1040 " pdb=" O VAL B1076 " model vdw 2.291 3.120 nonbonded pdb=" ND2 ASN A1040 " pdb=" O VAL A1076 " model vdw 2.292 3.120 ... (remaining 115392 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 34.730 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 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 : 0.011 0.100 14218 Z= 0.696 Angle : 0.927 11.687 19342 Z= 0.500 Chirality : 0.057 0.393 2288 Planarity : 0.006 0.065 2400 Dihedral : 13.500 104.395 5088 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.81 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.18), residues: 1780 helix: -0.37 (0.15), residues: 980 sheet: -1.64 (0.47), residues: 78 loop : -1.81 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 809 HIS 0.013 0.001 HIS A 790 PHE 0.034 0.003 PHE A 877 TYR 0.018 0.002 TYR A 663 ARG 0.071 0.002 ARG B 497 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.586 Fit side-chains REVERT: B 397 TRP cc_start: 0.7722 (m100) cc_final: 0.7509 (m100) REVERT: B 459 LYS cc_start: 0.8010 (mttt) cc_final: 0.7784 (mttp) REVERT: B 597 MET cc_start: 0.7873 (tpp) cc_final: 0.7636 (tpp) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.3102 time to fit residues: 137.2994 Evaluate side-chains 181 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 0.0050 chunk 92 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 163 optimal weight: 0.9980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 629 HIS B 752 ASN B 854 GLN B 882 HIS B1040 ASN A 629 HIS A 752 ASN A 882 HIS A1040 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14218 Z= 0.236 Angle : 0.642 10.222 19342 Z= 0.324 Chirality : 0.043 0.240 2288 Planarity : 0.004 0.045 2400 Dihedral : 7.040 68.939 2088 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.53 % Favored : 97.36 % Rotamer: Outliers : 2.08 % Allowed : 11.57 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.19), residues: 1780 helix: 0.64 (0.16), residues: 1006 sheet: -1.76 (0.46), residues: 92 loop : -1.37 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 649 HIS 0.005 0.001 HIS A 790 PHE 0.030 0.002 PHE A 877 TYR 0.030 0.002 TYR B 937 ARG 0.006 0.001 ARG B 497 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 218 time to evaluate : 1.486 Fit side-chains revert: symmetry clash REVERT: B 353 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6753 (mtpp) REVERT: A 626 ARG cc_start: 0.7650 (ttt-90) cc_final: 0.7033 (tpt90) REVERT: A 1070 TYR cc_start: 0.8684 (t80) cc_final: 0.8314 (t80) outliers start: 30 outliers final: 9 residues processed: 238 average time/residue: 0.2630 time to fit residues: 91.4218 Evaluate side-chains 188 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 178 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1039 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 45 optimal weight: 0.0050 chunk 163 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 HIS A 915 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14218 Z= 0.285 Angle : 0.622 10.387 19342 Z= 0.316 Chirality : 0.045 0.446 2288 Planarity : 0.004 0.037 2400 Dihedral : 5.863 66.472 2088 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.60 % Favored : 96.29 % Rotamer: Outliers : 2.42 % Allowed : 14.13 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.19), residues: 1780 helix: 0.90 (0.16), residues: 1008 sheet: -1.65 (0.49), residues: 92 loop : -1.24 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 704 HIS 0.003 0.001 HIS A 836 PHE 0.019 0.002 PHE A 877 TYR 0.030 0.002 TYR B 937 ARG 0.006 0.000 ARG B 624 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 187 time to evaluate : 1.549 Fit side-chains REVERT: B 353 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.6849 (mtpp) REVERT: A 116 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7388 (pt0) REVERT: A 626 ARG cc_start: 0.7689 (ttt-90) cc_final: 0.7089 (tpt90) REVERT: A 942 MET cc_start: 0.7130 (ppp) cc_final: 0.6576 (ptm) REVERT: A 1070 TYR cc_start: 0.8686 (t80) cc_final: 0.8328 (t80) outliers start: 35 outliers final: 20 residues processed: 210 average time/residue: 0.2381 time to fit residues: 75.0863 Evaluate side-chains 189 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 887 LYS Chi-restraints excluded: chain A residue 1039 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 164 optimal weight: 0.3980 chunk 173 optimal weight: 0.9990 chunk 85 optimal weight: 0.3980 chunk 155 optimal weight: 7.9990 chunk 46 optimal weight: 0.0040 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 382 GLN A 120 ASN A 844 ASN A 915 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 14218 Z= 0.195 Angle : 0.569 8.763 19342 Z= 0.288 Chirality : 0.043 0.356 2288 Planarity : 0.004 0.032 2400 Dihedral : 5.422 64.808 2088 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.74 % Rotamer: Outliers : 2.01 % Allowed : 15.30 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.20), residues: 1780 helix: 1.32 (0.16), residues: 996 sheet: -1.71 (0.45), residues: 112 loop : -1.07 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 649 HIS 0.003 0.001 HIS A 802 PHE 0.021 0.001 PHE A 442 TYR 0.029 0.001 TYR B 937 ARG 0.004 0.000 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 194 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7320 (pt0) REVERT: A 283 PHE cc_start: 0.8421 (t80) cc_final: 0.8061 (t80) REVERT: A 942 MET cc_start: 0.7221 (ppp) cc_final: 0.6914 (ptm) REVERT: A 1070 TYR cc_start: 0.8644 (t80) cc_final: 0.8116 (t80) outliers start: 29 outliers final: 18 residues processed: 216 average time/residue: 0.2278 time to fit residues: 74.9189 Evaluate side-chains 184 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 166 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 887 LYS Chi-restraints excluded: chain A residue 913 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 156 optimal weight: 0.0770 chunk 43 optimal weight: 0.6980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 14218 Z= 0.202 Angle : 0.565 8.354 19342 Z= 0.284 Chirality : 0.043 0.389 2288 Planarity : 0.004 0.047 2400 Dihedral : 5.262 63.701 2088 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.09 % Favored : 96.80 % Rotamer: Outliers : 1.66 % Allowed : 16.48 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.20), residues: 1780 helix: 1.45 (0.16), residues: 1002 sheet: -1.40 (0.50), residues: 92 loop : -0.96 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 649 HIS 0.003 0.001 HIS A 802 PHE 0.017 0.001 PHE A 442 TYR 0.029 0.001 TYR B 937 ARG 0.004 0.000 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 183 time to evaluate : 1.600 Fit side-chains revert: symmetry clash REVERT: B 708 LEU cc_start: 0.8836 (mt) cc_final: 0.8630 (mt) REVERT: A 283 PHE cc_start: 0.8420 (t80) cc_final: 0.8060 (t80) REVERT: A 384 ILE cc_start: 0.7534 (tp) cc_final: 0.7241 (tp) REVERT: A 626 ARG cc_start: 0.7673 (ttt-90) cc_final: 0.7145 (tpt90) REVERT: A 942 MET cc_start: 0.7321 (ppp) cc_final: 0.7000 (ptm) outliers start: 24 outliers final: 19 residues processed: 201 average time/residue: 0.2542 time to fit residues: 75.7883 Evaluate side-chains 188 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 169 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 178 CYS Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 887 LYS Chi-restraints excluded: chain A residue 913 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 915 HIS A1056 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14218 Z= 0.252 Angle : 0.585 8.084 19342 Z= 0.295 Chirality : 0.044 0.352 2288 Planarity : 0.004 0.038 2400 Dihedral : 5.238 63.251 2088 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.20 % Favored : 96.69 % Rotamer: Outliers : 2.08 % Allowed : 17.24 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.20), residues: 1780 helix: 1.57 (0.16), residues: 984 sheet: -1.47 (0.50), residues: 92 loop : -0.83 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 809 HIS 0.002 0.000 HIS A 802 PHE 0.017 0.001 PHE A 442 TYR 0.030 0.001 TYR B 937 ARG 0.004 0.000 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 174 time to evaluate : 1.561 Fit side-chains revert: symmetry clash REVERT: B 324 CYS cc_start: 0.6325 (OUTLIER) cc_final: 0.6021 (m) REVERT: B 325 MET cc_start: 0.7358 (mtm) cc_final: 0.7142 (mtp) REVERT: B 708 LEU cc_start: 0.8919 (mt) cc_final: 0.8702 (mt) REVERT: B 861 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.7016 (t0) REVERT: A 284 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7768 (pt) REVERT: A 626 ARG cc_start: 0.7706 (ttt-90) cc_final: 0.7180 (tpt90) REVERT: A 942 MET cc_start: 0.7307 (ppp) cc_final: 0.6872 (ptt) outliers start: 30 outliers final: 19 residues processed: 198 average time/residue: 0.2352 time to fit residues: 70.6851 Evaluate side-chains 187 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 165 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1056 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 127 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 105 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 HIS A1056 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 14218 Z= 0.239 Angle : 0.577 8.111 19342 Z= 0.291 Chirality : 0.043 0.360 2288 Planarity : 0.004 0.048 2400 Dihedral : 5.195 62.672 2088 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.74 % Rotamer: Outliers : 2.49 % Allowed : 17.59 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.20), residues: 1780 helix: 1.61 (0.16), residues: 984 sheet: -1.37 (0.45), residues: 128 loop : -0.82 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 809 HIS 0.003 0.000 HIS A 802 PHE 0.017 0.001 PHE A 442 TYR 0.029 0.001 TYR B 937 ARG 0.004 0.000 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 171 time to evaluate : 1.556 Fit side-chains revert: symmetry clash REVERT: B 324 CYS cc_start: 0.6348 (OUTLIER) cc_final: 0.6013 (m) REVERT: B 708 LEU cc_start: 0.8926 (mt) cc_final: 0.8711 (mt) REVERT: A 284 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7765 (pt) REVERT: A 384 ILE cc_start: 0.7517 (tp) cc_final: 0.7089 (tp) REVERT: A 626 ARG cc_start: 0.7701 (ttt-90) cc_final: 0.7172 (tpt90) REVERT: A 875 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7850 (mp) REVERT: A 942 MET cc_start: 0.7219 (ppp) cc_final: 0.6860 (ptt) REVERT: A 943 MET cc_start: 0.4616 (mmp) cc_final: 0.4391 (mmp) outliers start: 36 outliers final: 26 residues processed: 195 average time/residue: 0.2317 time to fit residues: 68.5577 Evaluate side-chains 197 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1039 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 0.0010 chunk 33 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 320 HIS A 120 ASN A 915 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14218 Z= 0.192 Angle : 0.564 7.984 19342 Z= 0.282 Chirality : 0.043 0.357 2288 Planarity : 0.004 0.043 2400 Dihedral : 5.079 61.816 2088 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.98 % Favored : 96.91 % Rotamer: Outliers : 1.87 % Allowed : 18.42 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.20), residues: 1780 helix: 1.76 (0.16), residues: 982 sheet: -1.37 (0.45), residues: 128 loop : -0.68 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 649 HIS 0.004 0.000 HIS A 802 PHE 0.023 0.001 PHE A 728 TYR 0.030 0.001 TYR B 937 ARG 0.005 0.000 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 182 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 324 CYS cc_start: 0.6321 (OUTLIER) cc_final: 0.6016 (m) REVERT: B 708 LEU cc_start: 0.8867 (mt) cc_final: 0.8659 (mt) REVERT: A 283 PHE cc_start: 0.8446 (t80) cc_final: 0.8029 (t80) REVERT: A 284 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7734 (pt) REVERT: A 384 ILE cc_start: 0.7581 (tp) cc_final: 0.7218 (tp) REVERT: A 626 ARG cc_start: 0.7684 (ttt-90) cc_final: 0.7159 (tpt90) REVERT: A 942 MET cc_start: 0.7195 (ppp) cc_final: 0.6911 (ptm) outliers start: 27 outliers final: 21 residues processed: 203 average time/residue: 0.2403 time to fit residues: 72.7347 Evaluate side-chains 199 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 638 SER Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1039 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 152 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 HIS A1056 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 14218 Z= 0.203 Angle : 0.577 10.909 19342 Z= 0.288 Chirality : 0.044 0.334 2288 Planarity : 0.004 0.040 2400 Dihedral : 5.048 61.236 2088 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.03 % Favored : 96.85 % Rotamer: Outliers : 1.73 % Allowed : 19.11 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.20), residues: 1780 helix: 1.80 (0.17), residues: 982 sheet: -1.37 (0.46), residues: 128 loop : -0.62 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 649 HIS 0.004 0.000 HIS A 867 PHE 0.019 0.001 PHE A 728 TYR 0.030 0.001 TYR B 937 ARG 0.005 0.000 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 324 CYS cc_start: 0.6352 (OUTLIER) cc_final: 0.6051 (m) REVERT: B 708 LEU cc_start: 0.8866 (mt) cc_final: 0.8659 (mt) REVERT: A 283 PHE cc_start: 0.8446 (t80) cc_final: 0.8049 (t80) REVERT: A 384 ILE cc_start: 0.7578 (tp) cc_final: 0.7210 (tp) REVERT: A 626 ARG cc_start: 0.7685 (ttt-90) cc_final: 0.7158 (tpt90) REVERT: A 942 MET cc_start: 0.7181 (ppp) cc_final: 0.6892 (ptt) REVERT: A 943 MET cc_start: 0.4605 (mmp) cc_final: 0.4383 (mmp) REVERT: A 1071 MET cc_start: 0.8956 (mmm) cc_final: 0.8417 (tpt) outliers start: 25 outliers final: 19 residues processed: 199 average time/residue: 0.2562 time to fit residues: 75.6177 Evaluate side-chains 197 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 177 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 913 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.0470 chunk 104 optimal weight: 0.0470 chunk 81 optimal weight: 6.9990 chunk 118 optimal weight: 0.4980 chunk 179 optimal weight: 1.9990 chunk 165 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 14 optimal weight: 0.0870 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 14218 Z= 0.166 Angle : 0.567 9.808 19342 Z= 0.283 Chirality : 0.043 0.333 2288 Planarity : 0.003 0.038 2400 Dihedral : 4.946 60.551 2088 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.75 % Favored : 97.13 % Rotamer: Outliers : 1.59 % Allowed : 19.32 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.20), residues: 1780 helix: 1.92 (0.16), residues: 982 sheet: -1.30 (0.45), residues: 128 loop : -0.52 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 649 HIS 0.004 0.000 HIS A 802 PHE 0.017 0.001 PHE A 442 TYR 0.030 0.001 TYR A1070 ARG 0.002 0.000 ARG A 917 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 185 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 871 MET cc_start: 0.7072 (mmm) cc_final: 0.6347 (mmp) REVERT: A 283 PHE cc_start: 0.8327 (t80) cc_final: 0.8019 (t80) REVERT: A 384 ILE cc_start: 0.7507 (tp) cc_final: 0.7159 (tp) REVERT: A 942 MET cc_start: 0.7154 (ppp) cc_final: 0.6795 (ptt) REVERT: A 1071 MET cc_start: 0.8941 (mmm) cc_final: 0.8409 (tpt) REVERT: A 1079 GLU cc_start: 0.7469 (tp30) cc_final: 0.6985 (tp30) outliers start: 23 outliers final: 16 residues processed: 201 average time/residue: 0.2507 time to fit residues: 75.3839 Evaluate side-chains 193 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 177 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 653 ILE Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 913 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 131 optimal weight: 0.7980 chunk 21 optimal weight: 0.0040 chunk 39 optimal weight: 0.0010 chunk 143 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 125 optimal weight: 0.0670 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 703 ASN A 120 ASN A 915 HIS ** A1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.180034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.134431 restraints weight = 16051.399| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.93 r_work: 0.3474 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 14218 Z= 0.161 Angle : 0.561 8.919 19342 Z= 0.280 Chirality : 0.043 0.347 2288 Planarity : 0.003 0.036 2400 Dihedral : 4.879 59.683 2088 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.64 % Favored : 97.25 % Rotamer: Outliers : 1.52 % Allowed : 19.25 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.20), residues: 1780 helix: 2.02 (0.17), residues: 984 sheet: -1.29 (0.44), residues: 128 loop : -0.46 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 649 HIS 0.004 0.000 HIS B 802 PHE 0.016 0.001 PHE A 442 TYR 0.030 0.001 TYR B 937 ARG 0.004 0.000 ARG B 626 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3222.14 seconds wall clock time: 59 minutes 16.63 seconds (3556.63 seconds total)