Starting phenix.real_space_refine on Sat Jan 20 00:24:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngb_12311/01_2024/7ngb_12311.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngb_12311/01_2024/7ngb_12311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngb_12311/01_2024/7ngb_12311.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngb_12311/01_2024/7ngb_12311.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngb_12311/01_2024/7ngb_12311.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngb_12311/01_2024/7ngb_12311.pdb" } resolution = 3.64 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= 0.042 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 86 5.16 5 C 8568 2.51 5 N 2178 2.21 5 O 2312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A GLU 696": "OE1" <-> "OE2" Residue "A ARG 917": "NH1" <-> "NH2" Residue "A GLU 1065": "OE1" <-> "OE2" Residue "A GLU 1079": "OE1" <-> "OE2" Residue "B PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 238": "OE1" <-> "OE2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B GLU 696": "OE1" <-> "OE2" Residue "B ARG 917": "NH1" <-> "NH2" Residue "B GLU 1065": "OE1" <-> "OE2" Residue "B GLU 1079": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13144 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6519 Classifications: {'peptide': 859} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 33, 'TRANS': 825} Chain breaks: 3 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 6519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6519 Classifications: {'peptide': 859} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 33, 'TRANS': 825} Chain breaks: 3 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 59 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: "D" 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: "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 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 Time building chain proxies: 7.32, per 1000 atoms: 0.56 Number of scatterers: 13144 At special positions: 0 Unit cell: (112.035, 103.499, 150.447, 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 86 16.00 O 2312 8.00 N 2178 7.00 C 8568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 640 " distance=2.05 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.02 Simple disulfide: pdb=" SG CYS A 359 " - pdb=" SG CYS A 369 " distance=2.02 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 640 " distance=2.05 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 339 " distance=2.02 Simple disulfide: pdb=" SG CYS B 359 " - pdb=" SG CYS B 369 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A1101 " - " ASN A 377 " " NAG B1101 " - " ASN B 377 " " NAG C 1 " - " ASN A 328 " " NAG D 1 " - " ASN B 328 " Time building additional restraints: 5.76 Conformation dependent library (CDL) restraints added in 2.4 seconds 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3156 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 8 sheets defined 61.6% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 135 through 149 removed outlier: 5.284A 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: 6.478A pdb=" N VAL A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 9.392A pdb=" N LEU A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLN A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 243 removed outlier: 3.571A 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 260 through 284 Processing helix chain 'A' and resid 285 through 314 removed outlier: 3.803A pdb=" N VAL A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N SER A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 4.998A 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 386 through 394 removed outlier: 4.204A pdb=" N GLY A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE A 391 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE A 392 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 393 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 removed outlier: 3.691A 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: 3.736A 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: 4.396A pdb=" N ILE A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 3.774A 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: 3.945A pdb=" N VAL A 558 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS A 561 " --> pdb=" O VAL A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 584 removed outlier: 3.547A pdb=" N LEU A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) removed outlier: 3.910A 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: 3.828A pdb=" N CYS A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 648 removed outlier: 3.572A pdb=" N SER A 633 " --> pdb=" O HIS A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 675 removed outlier: 3.630A pdb=" N ILE A 653 " --> pdb=" O TRP A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 696 removed outlier: 3.585A pdb=" N GLU A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 734 removed outlier: 4.293A 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: 4.034A pdb=" N GLN A 793 " --> pdb=" O SER A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 835 removed outlier: 3.597A pdb=" N PHE A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'A' and resid 868 through 881 removed outlier: 4.055A 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 901 through 917 removed outlier: 3.508A pdb=" N ARG A 917 " --> pdb=" O LEU A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1048 removed outlier: 3.939A 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 helix chain 'B' and resid 135 through 149 removed outlier: 5.283A 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: 6.480A pdb=" N VAL B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 9.393A pdb=" N LEU B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 243 removed outlier: 3.571A 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 260 through 284 Processing helix chain 'B' and resid 285 through 314 removed outlier: 3.802A pdb=" N VAL B 289 " --> pdb=" O GLY B 285 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N SER B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 4.999A 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 386 through 394 removed outlier: 4.204A pdb=" N GLY B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE B 391 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 392 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 393 " --> pdb=" O GLY B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 removed outlier: 3.691A 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: 3.736A 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: 4.396A pdb=" N ILE B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 3.774A 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: 3.944A pdb=" N VAL B 558 " --> pdb=" O PHE B 555 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS B 561 " --> pdb=" O VAL B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 584 removed outlier: 3.547A pdb=" N LEU B 572 " --> pdb=" O PRO B 568 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 3.910A 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: 3.828A pdb=" N CYS B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 648 removed outlier: 3.572A pdb=" N SER B 633 " --> pdb=" O HIS B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 675 removed outlier: 3.631A pdb=" N ILE B 653 " --> pdb=" O TRP B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 696 removed outlier: 3.585A pdb=" N GLU B 696 " --> pdb=" O LEU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 734 removed outlier: 4.293A 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: 4.034A pdb=" N GLN B 793 " --> pdb=" O SER B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 835 removed outlier: 3.598A pdb=" N PHE B 825 " --> pdb=" O ALA B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 848 Processing helix chain 'B' and resid 868 through 881 removed outlier: 4.055A 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 901 through 917 removed outlier: 3.508A pdb=" N ARG B 917 " --> pdb=" O LEU B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1048 removed outlier: 3.939A 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 sheet with id=AA1, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA2, first strand: chain 'A' and resid 342 through 345 removed outlier: 3.622A pdb=" N VAL A 350 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 775 through 781 removed outlier: 6.771A pdb=" N LEU A 708 " --> pdb=" O ILE A 740 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLY A 742 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL A 710 " --> pdb=" O GLY A 742 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL A 744 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLY A 808 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A1084 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL A1053 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL A1087 " --> pdb=" O VAL A1053 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU A1055 " --> pdb=" O VAL A1087 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 859 through 860 removed outlier: 6.691A pdb=" N ILE A 890 " --> pdb=" O GLU A 921 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N GLU A 923 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE A 892 " --> pdb=" O GLU A 923 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 329 through 330 Processing sheet with id=AA6, first strand: chain 'B' and resid 342 through 345 removed outlier: 3.622A pdb=" N VAL B 350 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 775 through 781 removed outlier: 6.772A pdb=" N LEU B 708 " --> pdb=" O ILE B 740 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLY B 742 " --> pdb=" O LEU B 708 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL B 710 " --> pdb=" O GLY B 742 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL B 744 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLY B 808 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B1084 " --> pdb=" O LYS B 843 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL B1053 " --> pdb=" O LEU B1085 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL B1087 " --> pdb=" O VAL B1053 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU B1055 " --> pdb=" O VAL B1087 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 859 through 860 removed outlier: 6.691A pdb=" N ILE B 890 " --> pdb=" O GLU B 921 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N GLU B 923 " --> pdb=" O ILE B 890 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ILE B 892 " --> pdb=" O GLU B 923 " (cutoff:3.500A) 786 hydrogen bonds defined for protein. 2262 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: 4.66 Time building geometry restraints manager: 6.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 2945 1.33 - 1.46: 4321 1.46 - 1.60: 6050 1.60 - 1.73: 0 1.73 - 1.87: 134 Bond restraints: 13450 Sorted by residual: bond pdb=" N ILE B 918 " pdb=" CA ILE B 918 " ideal model delta sigma weight residual 1.458 1.499 -0.042 1.14e-02 7.69e+03 1.36e+01 bond pdb=" N ILE A 918 " pdb=" CA ILE A 918 " ideal model delta sigma weight residual 1.458 1.499 -0.042 1.14e-02 7.69e+03 1.33e+01 bond pdb=" C PHE B 274 " pdb=" O PHE B 274 " ideal model delta sigma weight residual 1.237 1.194 0.042 1.17e-02 7.31e+03 1.31e+01 bond pdb=" C PHE A 274 " pdb=" O PHE A 274 " ideal model delta sigma weight residual 1.237 1.195 0.042 1.17e-02 7.31e+03 1.30e+01 bond pdb=" C ASP B 908 " pdb=" O ASP B 908 " ideal model delta sigma weight residual 1.237 1.276 -0.040 1.17e-02 7.31e+03 1.15e+01 ... (remaining 13445 not shown) Histogram of bond angle deviations from ideal: 97.69 - 105.00: 257 105.00 - 112.31: 7047 112.31 - 119.61: 4626 119.61 - 126.92: 6179 126.92 - 134.22: 195 Bond angle restraints: 18304 Sorted by residual: angle pdb=" N GLN A 904 " pdb=" CA GLN A 904 " pdb=" C GLN A 904 " ideal model delta sigma weight residual 111.28 104.98 6.30 1.09e+00 8.42e-01 3.34e+01 angle pdb=" N GLN B 904 " pdb=" CA GLN B 904 " pdb=" C GLN B 904 " ideal model delta sigma weight residual 111.28 104.99 6.29 1.09e+00 8.42e-01 3.33e+01 angle pdb=" CA TRP A 864 " pdb=" C TRP A 864 " pdb=" O TRP A 864 " ideal model delta sigma weight residual 122.37 116.78 5.59 1.15e+00 7.56e-01 2.37e+01 angle pdb=" CA TRP B 864 " pdb=" C TRP B 864 " pdb=" O TRP B 864 " ideal model delta sigma weight residual 122.37 116.79 5.58 1.15e+00 7.56e-01 2.36e+01 angle pdb=" C ILE A 639 " pdb=" N CYS A 640 " pdb=" CA CYS A 640 " ideal model delta sigma weight residual 122.38 114.41 7.97 1.81e+00 3.05e-01 1.94e+01 ... (remaining 18299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.80: 7502 20.80 - 41.60: 356 41.60 - 62.40: 72 62.40 - 83.20: 18 83.20 - 104.00: 10 Dihedral angle restraints: 7958 sinusoidal: 3048 harmonic: 4910 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 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+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 180.00 155.01 24.99 0 5.00e+00 4.00e-02 2.50e+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 58.58 34.42 1 1.00e+01 1.00e-02 1.68e+01 ... (remaining 7955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1825 0.090 - 0.181: 327 0.181 - 0.271: 20 0.271 - 0.361: 4 0.361 - 0.451: 2 Chirality restraints: 2178 Sorted by residual: chirality pdb=" C1 NAG A1101 " pdb=" ND2 ASN A 377 " pdb=" C2 NAG A1101 " pdb=" O5 NAG A1101 " both_signs ideal model delta sigma weight residual False -2.40 -2.85 0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" C1 NAG B1101 " pdb=" ND2 ASN B 377 " pdb=" C2 NAG B1101 " pdb=" O5 NAG B1101 " both_signs ideal model delta sigma weight residual False -2.40 -2.85 0.45 2.00e-01 2.50e+01 5.07e+00 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 2.15 0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 2175 not shown) Planarity restraints: 2270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 497 " 0.082 9.50e-02 1.11e+02 4.99e-02 1.50e+01 pdb=" NE ARG A 497 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A 497 " 0.064 2.00e-02 2.50e+03 pdb=" NH1 ARG A 497 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG A 497 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 497 " -0.083 9.50e-02 1.11e+02 5.00e-02 1.49e+01 pdb=" NE ARG B 497 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG B 497 " -0.064 2.00e-02 2.50e+03 pdb=" NH1 ARG B 497 " 0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG B 497 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 240 " -0.018 2.00e-02 2.50e+03 3.64e-02 1.33e+01 pdb=" C PHE B 240 " 0.063 2.00e-02 2.50e+03 pdb=" O PHE B 240 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU B 241 " -0.021 2.00e-02 2.50e+03 ... (remaining 2267 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3512 2.80 - 3.32: 13418 3.32 - 3.85: 21359 3.85 - 4.37: 24132 4.37 - 4.90: 41312 Nonbonded interactions: 103733 Sorted by model distance: nonbonded pdb=" O THR B 431 " pdb=" OG1 THR B 431 " model vdw 2.269 2.440 nonbonded pdb=" O THR A 431 " pdb=" OG1 THR A 431 " model vdw 2.270 2.440 nonbonded pdb=" O PRO A 698 " pdb=" NH1 ARG B 680 " model vdw 2.279 2.520 nonbonded pdb=" OD1 ASP B 715 " pdb=" N HIS B 719 " model vdw 2.280 2.520 nonbonded pdb=" OD1 ASP A 715 " pdb=" N HIS A 719 " model vdw 2.281 2.520 ... (remaining 103728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 2.070 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: 7.470 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 38.360 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.090 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 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 : 0.010 0.074 13450 Z= 0.637 Angle : 1.079 9.765 18304 Z= 0.640 Chirality : 0.067 0.451 2178 Planarity : 0.007 0.056 2266 Dihedral : 13.737 103.995 4784 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.47 % Favored : 97.41 % Rotamer: Outliers : 0.59 % Allowed : 6.52 % Favored : 92.90 % 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: -1.80 (0.18), residues: 1702 helix: -0.64 (0.15), residues: 954 sheet: -1.70 (0.46), residues: 92 loop : -1.81 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP B 822 HIS 0.009 0.002 HIS B 790 PHE 0.033 0.004 PHE B 441 TYR 0.023 0.003 TYR B 222 ARG 0.065 0.002 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 277 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 MET cc_start: 0.8000 (tpp) cc_final: 0.7644 (tpp) REVERT: A 917 ARG cc_start: 0.5905 (OUTLIER) cc_final: 0.5372 (mtt180) REVERT: A 923 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6420 (tm-30) REVERT: A 1045 ASN cc_start: 0.8242 (m-40) cc_final: 0.7938 (t0) REVERT: B 263 MET cc_start: 0.7204 (tpp) cc_final: 0.6947 (tpp) REVERT: B 601 MET cc_start: 0.7882 (tpp) cc_final: 0.7608 (tpp) REVERT: B 626 ARG cc_start: 0.7003 (ttt-90) cc_final: 0.6581 (tpt170) REVERT: B 917 ARG cc_start: 0.5838 (OUTLIER) cc_final: 0.5283 (mtt180) REVERT: B 923 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6580 (tm-30) REVERT: B 1081 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6097 (mp) outliers start: 8 outliers final: 0 residues processed: 281 average time/residue: 0.2598 time to fit residues: 105.3831 Evaluate side-chains 166 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 161 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 917 ARG Chi-restraints excluded: chain A residue 923 GLU Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 923 GLU Chi-restraints excluded: chain B residue 1081 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.0270 chunk 128 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 133 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 HIS A 613 GLN A 731 GLN B 146 GLN B 290 ASN B 423 HIS B 613 GLN B 731 GLN B1069 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13450 Z= 0.202 Angle : 0.632 10.405 18304 Z= 0.321 Chirality : 0.044 0.252 2178 Planarity : 0.004 0.048 2266 Dihedral : 8.116 55.775 1996 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.82 % Favored : 97.06 % Rotamer: Outliers : 1.54 % Allowed : 13.54 % Favored : 84.92 % 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: -0.03 (0.20), residues: 1702 helix: 1.05 (0.16), residues: 934 sheet: -1.17 (0.50), residues: 92 loop : -1.37 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 822 HIS 0.006 0.001 HIS B 423 PHE 0.016 0.002 PHE B 357 TYR 0.015 0.001 TYR B 202 ARG 0.002 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 217 time to evaluate : 1.457 Fit side-chains revert: symmetry clash REVERT: A 917 ARG cc_start: 0.5531 (OUTLIER) cc_final: 0.5183 (mmt90) REVERT: A 1045 ASN cc_start: 0.8179 (m-40) cc_final: 0.7903 (t0) REVERT: B 626 ARG cc_start: 0.7055 (ttt-90) cc_final: 0.6728 (tpt170) REVERT: B 728 PHE cc_start: 0.7394 (t80) cc_final: 0.7146 (t80) REVERT: B 1057 MET cc_start: 0.6450 (mtp) cc_final: 0.5972 (mtp) REVERT: B 1081 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6676 (mp) outliers start: 21 outliers final: 5 residues processed: 233 average time/residue: 0.2037 time to fit residues: 75.0455 Evaluate side-chains 181 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 174 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 917 ARG Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 1081 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 42 optimal weight: 0.4980 chunk 154 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1069 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13450 Z= 0.198 Angle : 0.612 9.922 18304 Z= 0.305 Chirality : 0.044 0.295 2178 Planarity : 0.004 0.049 2266 Dihedral : 6.296 54.470 1986 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.94 % Favored : 96.94 % Rotamer: Outliers : 2.71 % Allowed : 15.45 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.51 (0.20), residues: 1702 helix: 1.53 (0.17), residues: 932 sheet: -0.78 (0.53), residues: 92 loop : -1.21 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 809 HIS 0.007 0.001 HIS B 915 PHE 0.021 0.001 PHE A 728 TYR 0.013 0.001 TYR B 202 ARG 0.002 0.000 ARG B1062 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 192 time to evaluate : 1.468 Fit side-chains revert: symmetry clash REVERT: A 601 MET cc_start: 0.7805 (tpp) cc_final: 0.7417 (tpp) REVERT: A 634 PHE cc_start: 0.8677 (t80) cc_final: 0.8321 (t80) REVERT: B 626 ARG cc_start: 0.7060 (ttt-90) cc_final: 0.6736 (tpt170) REVERT: B 728 PHE cc_start: 0.7440 (t80) cc_final: 0.7189 (t80) REVERT: B 1081 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.6957 (mp) outliers start: 37 outliers final: 15 residues processed: 217 average time/residue: 0.1947 time to fit residues: 68.6332 Evaluate side-chains 180 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 800 MET Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain B residue 1081 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.0770 chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 164 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN A 765 HIS B 382 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13450 Z= 0.189 Angle : 0.601 9.853 18304 Z= 0.298 Chirality : 0.044 0.265 2178 Planarity : 0.004 0.044 2266 Dihedral : 5.378 53.384 1982 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.17 % Favored : 96.71 % Rotamer: Outliers : 2.12 % Allowed : 17.72 % Favored : 80.16 % 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: 0.80 (0.20), residues: 1702 helix: 1.74 (0.17), residues: 928 sheet: -0.68 (0.52), residues: 92 loop : -1.02 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 813 HIS 0.007 0.001 HIS B 915 PHE 0.016 0.001 PHE A 877 TYR 0.015 0.001 TYR B 202 ARG 0.002 0.000 ARG B1062 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 185 time to evaluate : 1.340 Fit side-chains revert: symmetry clash REVERT: A 601 MET cc_start: 0.8086 (tpp) cc_final: 0.7468 (tpp) REVERT: B 597 MET cc_start: 0.7892 (tpp) cc_final: 0.7565 (tpp) REVERT: B 601 MET cc_start: 0.7839 (tpp) cc_final: 0.7299 (tpp) REVERT: B 626 ARG cc_start: 0.7039 (ttt-90) cc_final: 0.6736 (tpt170) REVERT: B 634 PHE cc_start: 0.8590 (t80) cc_final: 0.8205 (t80) REVERT: B 1081 LEU cc_start: 0.7417 (tp) cc_final: 0.6810 (mp) outliers start: 29 outliers final: 15 residues processed: 208 average time/residue: 0.1830 time to fit residues: 62.4538 Evaluate side-chains 181 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 800 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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: 0.7301 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13450 Z= 0.283 Angle : 0.645 9.140 18304 Z= 0.325 Chirality : 0.046 0.264 2178 Planarity : 0.004 0.044 2266 Dihedral : 5.082 51.935 1980 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.82 % Favored : 96.06 % Rotamer: Outliers : 2.93 % Allowed : 19.40 % Favored : 77.67 % 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: 0.76 (0.20), residues: 1702 helix: 1.66 (0.17), residues: 930 sheet: -1.04 (0.50), residues: 96 loop : -0.90 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 813 HIS 0.019 0.002 HIS A 915 PHE 0.026 0.002 PHE A 728 TYR 0.014 0.002 TYR A 202 ARG 0.003 0.000 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 172 time to evaluate : 1.591 Fit side-chains REVERT: A 280 LEU cc_start: 0.8143 (pp) cc_final: 0.7889 (pp) REVERT: A 601 MET cc_start: 0.8183 (tpp) cc_final: 0.7701 (tpp) REVERT: B 601 MET cc_start: 0.7967 (tpp) cc_final: 0.7573 (tpp) REVERT: B 626 ARG cc_start: 0.7093 (ttt-90) cc_final: 0.6821 (tpt170) REVERT: B 638 SER cc_start: 0.8662 (p) cc_final: 0.8178 (p) REVERT: B 743 SER cc_start: 0.8059 (OUTLIER) cc_final: 0.7623 (p) REVERT: B 1081 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.6883 (mp) outliers start: 40 outliers final: 22 residues processed: 200 average time/residue: 0.1849 time to fit residues: 60.8132 Evaluate side-chains 183 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 901 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 800 MET Chi-restraints excluded: chain B residue 1067 ASP Chi-restraints excluded: chain B residue 1081 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 164 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7255 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13450 Z= 0.192 Angle : 0.601 9.283 18304 Z= 0.300 Chirality : 0.043 0.254 2178 Planarity : 0.004 0.047 2266 Dihedral : 4.869 52.640 1980 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.65 % Rotamer: Outliers : 2.27 % Allowed : 18.89 % Favored : 78.84 % 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: 0.93 (0.21), residues: 1702 helix: 1.86 (0.17), residues: 926 sheet: -1.10 (0.49), residues: 96 loop : -0.88 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 813 HIS 0.006 0.001 HIS B 915 PHE 0.028 0.001 PHE A 728 TYR 0.013 0.001 TYR A 202 ARG 0.002 0.000 ARG B 814 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 1.452 Fit side-chains REVERT: A 181 MET cc_start: 0.8206 (tpt) cc_final: 0.7985 (tpp) REVERT: A 280 LEU cc_start: 0.7975 (pp) cc_final: 0.7719 (pp) REVERT: A 601 MET cc_start: 0.8105 (tpp) cc_final: 0.7704 (tpp) REVERT: A 901 ASN cc_start: 0.5533 (OUTLIER) cc_final: 0.4717 (p0) REVERT: B 280 LEU cc_start: 0.8086 (pp) cc_final: 0.7825 (pp) REVERT: B 601 MET cc_start: 0.7874 (tpp) cc_final: 0.7500 (tpp) REVERT: B 626 ARG cc_start: 0.7095 (ttt-90) cc_final: 0.6823 (tpt170) REVERT: B 728 PHE cc_start: 0.7281 (t80) cc_final: 0.6983 (t80) REVERT: B 901 ASN cc_start: 0.5485 (OUTLIER) cc_final: 0.4523 (p0) REVERT: B 917 ARG cc_start: 0.5360 (OUTLIER) cc_final: 0.4959 (mmt90) REVERT: B 1081 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.6848 (mp) outliers start: 31 outliers final: 15 residues processed: 203 average time/residue: 0.1865 time to fit residues: 62.1631 Evaluate side-chains 177 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 158 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 901 ASN Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 800 MET Chi-restraints excluded: chain B residue 901 ASN Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 1067 ASP Chi-restraints excluded: chain B residue 1081 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 91 optimal weight: 0.0970 chunk 163 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 765 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13450 Z= 0.209 Angle : 0.617 13.057 18304 Z= 0.307 Chirality : 0.044 0.272 2178 Planarity : 0.004 0.045 2266 Dihedral : 4.801 52.434 1980 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.35 % Favored : 96.53 % Rotamer: Outliers : 2.78 % Allowed : 18.96 % Favored : 78.26 % 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 (0.21), residues: 1702 helix: 1.88 (0.17), residues: 926 sheet: -1.26 (0.49), residues: 96 loop : -0.89 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 813 HIS 0.006 0.001 HIS B 915 PHE 0.025 0.001 PHE A 728 TYR 0.012 0.001 TYR A 202 ARG 0.003 0.000 ARG B 814 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 171 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.8258 (tpt) cc_final: 0.8012 (tpp) REVERT: A 280 LEU cc_start: 0.8000 (pp) cc_final: 0.7740 (pp) REVERT: A 601 MET cc_start: 0.8121 (tpp) cc_final: 0.7702 (tpp) REVERT: A 743 SER cc_start: 0.8137 (OUTLIER) cc_final: 0.7679 (p) REVERT: A 901 ASN cc_start: 0.5527 (OUTLIER) cc_final: 0.4565 (p0) REVERT: B 181 MET cc_start: 0.8185 (tpt) cc_final: 0.7916 (tpp) REVERT: B 280 LEU cc_start: 0.7871 (pp) cc_final: 0.7615 (pp) REVERT: B 471 LEU cc_start: 0.8599 (mm) cc_final: 0.7502 (tp) REVERT: B 601 MET cc_start: 0.7893 (tpp) cc_final: 0.7501 (tpp) REVERT: B 626 ARG cc_start: 0.7165 (ttt-90) cc_final: 0.6854 (tpt170) REVERT: B 728 PHE cc_start: 0.7463 (t80) cc_final: 0.7157 (t80) REVERT: B 874 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7677 (tt) REVERT: B 901 ASN cc_start: 0.5650 (OUTLIER) cc_final: 0.4576 (p0) REVERT: B 917 ARG cc_start: 0.5353 (OUTLIER) cc_final: 0.4989 (mmt90) REVERT: B 1081 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.6849 (mp) outliers start: 38 outliers final: 24 residues processed: 200 average time/residue: 0.1890 time to fit residues: 61.4420 Evaluate side-chains 194 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 901 ASN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 800 MET Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 901 ASN Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 1067 ASP Chi-restraints excluded: chain B residue 1081 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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: 0.7348 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13450 Z= 0.310 Angle : 0.670 9.232 18304 Z= 0.341 Chirality : 0.046 0.276 2178 Planarity : 0.004 0.045 2266 Dihedral : 4.971 51.656 1980 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.11 % Favored : 95.77 % Rotamer: Outliers : 2.49 % Allowed : 19.40 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1702 helix: 1.58 (0.17), residues: 942 sheet: -1.76 (0.47), residues: 96 loop : -1.00 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 813 HIS 0.006 0.001 HIS A 802 PHE 0.023 0.002 PHE A 728 TYR 0.017 0.002 TYR B 222 ARG 0.004 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 168 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: A 181 MET cc_start: 0.8288 (tpt) cc_final: 0.8085 (tpp) REVERT: A 280 LEU cc_start: 0.7954 (pp) cc_final: 0.7692 (pp) REVERT: A 471 LEU cc_start: 0.8556 (mm) cc_final: 0.7310 (tp) REVERT: A 601 MET cc_start: 0.8095 (tpp) cc_final: 0.7763 (tpp) REVERT: B 181 MET cc_start: 0.8273 (tpt) cc_final: 0.8057 (tpp) REVERT: B 280 LEU cc_start: 0.7983 (pp) cc_final: 0.7727 (pp) REVERT: B 601 MET cc_start: 0.7916 (tpp) cc_final: 0.7424 (tpp) REVERT: B 626 ARG cc_start: 0.7217 (ttt-90) cc_final: 0.6857 (tpt90) REVERT: B 874 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7866 (tt) REVERT: B 901 ASN cc_start: 0.5591 (OUTLIER) cc_final: 0.4577 (p0) REVERT: B 917 ARG cc_start: 0.5535 (OUTLIER) cc_final: 0.5081 (mmt90) REVERT: B 1081 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.6743 (mp) outliers start: 34 outliers final: 25 residues processed: 194 average time/residue: 0.1873 time to fit residues: 58.9636 Evaluate side-chains 186 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 157 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 924 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 800 MET Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 901 ASN Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 1067 ASP Chi-restraints excluded: chain B residue 1081 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.0060 chunk 143 optimal weight: 0.0980 chunk 152 optimal weight: 0.4980 chunk 91 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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: 0.7256 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13450 Z= 0.175 Angle : 0.628 15.940 18304 Z= 0.309 Chirality : 0.044 0.264 2178 Planarity : 0.004 0.043 2266 Dihedral : 4.730 53.140 1980 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.00 % Favored : 96.89 % Rotamer: Outliers : 1.90 % Allowed : 20.35 % Favored : 77.75 % 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: 0.88 (0.21), residues: 1702 helix: 1.86 (0.17), residues: 928 sheet: -1.47 (0.47), residues: 104 loop : -0.90 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 813 HIS 0.002 0.000 HIS B 802 PHE 0.019 0.001 PHE A 877 TYR 0.012 0.001 TYR B 202 ARG 0.002 0.000 ARG B 814 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 168 time to evaluate : 1.439 Fit side-chains REVERT: A 181 MET cc_start: 0.8267 (tpt) cc_final: 0.8051 (tpp) REVERT: A 280 LEU cc_start: 0.8011 (pp) cc_final: 0.7755 (pp) REVERT: A 471 LEU cc_start: 0.8553 (mm) cc_final: 0.7337 (tp) REVERT: A 601 MET cc_start: 0.8029 (tpp) cc_final: 0.7697 (tpp) REVERT: B 181 MET cc_start: 0.8235 (tpt) cc_final: 0.8004 (tpp) REVERT: B 280 LEU cc_start: 0.7898 (pp) cc_final: 0.7656 (pp) REVERT: B 471 LEU cc_start: 0.8533 (mm) cc_final: 0.7287 (tp) REVERT: B 601 MET cc_start: 0.7968 (tpp) cc_final: 0.7442 (tpp) REVERT: B 626 ARG cc_start: 0.7215 (ttt-90) cc_final: 0.6854 (tpt90) REVERT: B 874 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7804 (tt) REVERT: B 901 ASN cc_start: 0.5367 (OUTLIER) cc_final: 0.4370 (p0) REVERT: B 917 ARG cc_start: 0.5520 (OUTLIER) cc_final: 0.5064 (mmt90) REVERT: B 1081 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6817 (mp) outliers start: 26 outliers final: 20 residues processed: 188 average time/residue: 0.1908 time to fit residues: 58.0170 Evaluate side-chains 185 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 161 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 800 MET Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 901 ASN Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 1067 ASP Chi-restraints excluded: chain B residue 1081 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.8980 chunk 76 optimal weight: 0.0670 chunk 112 optimal weight: 7.9990 chunk 169 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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: 0.7255 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13450 Z= 0.184 Angle : 0.622 15.447 18304 Z= 0.307 Chirality : 0.044 0.257 2178 Planarity : 0.004 0.044 2266 Dihedral : 4.646 52.987 1980 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.77 % Rotamer: Outliers : 1.68 % Allowed : 21.16 % Favored : 77.16 % 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: 0.96 (0.21), residues: 1702 helix: 1.90 (0.17), residues: 936 sheet: -1.33 (0.47), residues: 104 loop : -0.88 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 813 HIS 0.003 0.001 HIS B 790 PHE 0.021 0.001 PHE B 728 TYR 0.012 0.001 TYR B 222 ARG 0.002 0.000 ARG A 785 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 163 time to evaluate : 1.447 Fit side-chains revert: symmetry clash REVERT: A 181 MET cc_start: 0.8198 (tpt) cc_final: 0.7971 (tpp) REVERT: A 280 LEU cc_start: 0.8032 (pp) cc_final: 0.7778 (pp) REVERT: A 471 LEU cc_start: 0.8507 (mm) cc_final: 0.7322 (tp) REVERT: A 601 MET cc_start: 0.7992 (tpp) cc_final: 0.7736 (tpp) REVERT: B 181 MET cc_start: 0.8135 (tpt) cc_final: 0.7913 (tpp) REVERT: B 280 LEU cc_start: 0.7928 (pp) cc_final: 0.7692 (pp) REVERT: B 471 LEU cc_start: 0.8511 (mm) cc_final: 0.7287 (tp) REVERT: B 601 MET cc_start: 0.7989 (tpp) cc_final: 0.7020 (tpp) REVERT: B 626 ARG cc_start: 0.7228 (ttt-90) cc_final: 0.6852 (tpt90) REVERT: B 874 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7880 (tt) REVERT: B 901 ASN cc_start: 0.5261 (OUTLIER) cc_final: 0.4304 (p0) REVERT: B 917 ARG cc_start: 0.5472 (OUTLIER) cc_final: 0.5006 (mmt90) REVERT: B 1081 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.6975 (mp) outliers start: 23 outliers final: 17 residues processed: 179 average time/residue: 0.1981 time to fit residues: 57.5089 Evaluate side-chains 178 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 157 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 778 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 800 MET Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 901 ASN Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 1081 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 135 optimal weight: 0.6980 chunk 56 optimal weight: 0.0000 chunk 138 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 = 0.4262 r_free = 0.4262 target = 0.157893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.119843 restraints weight = 17927.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.125432 restraints weight = 9089.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.129417 restraints weight = 5875.020| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13450 Z= 0.181 Angle : 0.624 11.164 18304 Z= 0.307 Chirality : 0.044 0.251 2178 Planarity : 0.004 0.043 2266 Dihedral : 4.624 53.071 1980 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.00 % Favored : 96.89 % Rotamer: Outliers : 1.61 % Allowed : 21.23 % Favored : 77.16 % 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: 1.03 (0.21), residues: 1702 helix: 1.94 (0.17), residues: 936 sheet: -1.25 (0.47), residues: 104 loop : -0.83 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 813 HIS 0.002 0.000 HIS A 802 PHE 0.025 0.001 PHE B 149 TYR 0.012 0.001 TYR B 222 ARG 0.002 0.000 ARG B 814 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2526.28 seconds wall clock time: 46 minutes 54.22 seconds (2814.22 seconds total)