Starting phenix.real_space_refine on Sun Jun 29 17:37:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g27_29678/06_2025/8g27_29678.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g27_29678/06_2025/8g27_29678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g27_29678/06_2025/8g27_29678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g27_29678/06_2025/8g27_29678.map" model { file = "/net/cci-nas-00/data/ceres_data/8g27_29678/06_2025/8g27_29678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g27_29678/06_2025/8g27_29678.cif" } resolution = 3.3 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= -0.000 sd= 1.000 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 6 5.21 5 S 87 5.16 5 C 11419 2.51 5 N 2884 2.21 5 O 3119 1.98 5 H 16885 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34406 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 11356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 11356 Classifications: {'peptide': 718} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 673} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 11394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 11394 Classifications: {'peptide': 720} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 675} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 11372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 11372 Classifications: {'peptide': 719} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 674} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2, 'water': 2} Link IDs: {None: 3} Time building chain proxies: 18.69, per 1000 atoms: 0.54 Number of scatterers: 34406 At special positions: 0 Unit cell: (109.12, 134.64, 139.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 87 16.00 P 6 15.00 Mg 6 11.99 O 3119 8.00 N 2884 7.00 C 11419 6.00 H 16885 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=1, symmetry=0 Links applied BETA1-4 " BGC A 1 " - " BGC A 2 " " BGC A 2 " - " BGC A 3 " " BGC A 3 " - " BGC A 4 " " BGC A 4 " - " BGC A 5 " " BGC B 1 " - " BGC B 2 " " BGC B 2 " - " BGC B 3 " " BGC B 3 " - " BGC B 4 " " BGC B 4 " - " BGC B 5 " " BGC E 1 " - " BGC E 2 " " BGC E 2 " - " BGC E 3 " " BGC E 3 " - " BGC E 4 " " BGC E 4 " - " BGC E 5 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.64 Conformation dependent library (CDL) restraints added in 2.6 seconds 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4002 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 8 sheets defined 56.7% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'D' and resid 170 through 194 removed outlier: 3.548A pdb=" N ILE D 177 " --> pdb=" O TYR D 173 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE D 182 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN D 194 " --> pdb=" O TYR D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 222 removed outlier: 3.566A pdb=" N VAL D 207 " --> pdb=" O TRP D 203 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE D 222 " --> pdb=" O VAL D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 234 through 242 Processing helix chain 'D' and resid 266 through 278 removed outlier: 4.179A pdb=" N THR D 270 " --> pdb=" O PRO D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 322 removed outlier: 3.565A pdb=" N PHE D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LYS D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Proline residue: D 316 - end of helix Processing helix chain 'D' and resid 327 through 333 removed outlier: 3.802A pdb=" N SER D 333 " --> pdb=" O GLU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 372 removed outlier: 3.612A pdb=" N GLU D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 451 Processing helix chain 'D' and resid 469 through 479 removed outlier: 4.084A pdb=" N ILE D 477 " --> pdb=" O GLU D 473 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU D 478 " --> pdb=" O ALA D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 515 removed outlier: 3.995A pdb=" N PHE D 513 " --> pdb=" O ASN D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 521 Processing helix chain 'D' and resid 537 through 542 removed outlier: 3.579A pdb=" N GLY D 542 " --> pdb=" O GLN D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 619 Processing helix chain 'D' and resid 621 through 628 removed outlier: 3.534A pdb=" N ILE D 625 " --> pdb=" O SER D 621 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR D 628 " --> pdb=" O PHE D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 651 removed outlier: 3.530A pdb=" N LEU D 644 " --> pdb=" O ASN D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 685 removed outlier: 4.000A pdb=" N LEU D 678 " --> pdb=" O THR D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 727 removed outlier: 3.531A pdb=" N PHE D 727 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 756 Processing helix chain 'D' and resid 759 through 776 removed outlier: 3.632A pdb=" N LEU D 763 " --> pdb=" O THR D 759 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE D 769 " --> pdb=" O ALA D 765 " (cutoff:3.500A) Proline residue: D 770 - end of helix Processing helix chain 'D' and resid 787 through 811 Processing helix chain 'D' and resid 813 through 846 removed outlier: 3.826A pdb=" N ILE D 826 " --> pdb=" O GLN D 822 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER D 830 " --> pdb=" O ILE D 826 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS D 832 " --> pdb=" O GLY D 828 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU D 833 " --> pdb=" O VAL D 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 875 removed outlier: 3.666A pdb=" N LEU D 875 " --> pdb=" O TRP D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 875 through 899 removed outlier: 3.642A pdb=" N THR D 879 " --> pdb=" O LEU D 875 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 894 " --> pdb=" O VAL D 890 " (cutoff:3.500A) Processing helix chain 'D' and resid 905 through 928 Proline residue: D 923 - end of helix Processing helix chain 'D' and resid 939 through 954 removed outlier: 3.835A pdb=" N SER D 943 " --> pdb=" O VAL D 939 " (cutoff:3.500A) Processing helix chain 'I' and resid 170 through 193 removed outlier: 3.565A pdb=" N ILE I 177 " --> pdb=" O TYR I 173 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE I 182 " --> pdb=" O ILE I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 222 removed outlier: 3.709A pdb=" N PHE I 222 " --> pdb=" O VAL I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 225 No H-bonds generated for 'chain 'I' and resid 223 through 225' Processing helix chain 'I' and resid 234 through 242 Processing helix chain 'I' and resid 266 through 278 removed outlier: 4.193A pdb=" N THR I 270 " --> pdb=" O PRO I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 322 removed outlier: 3.562A pdb=" N PHE I 301 " --> pdb=" O ALA I 297 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG I 312 " --> pdb=" O ALA I 308 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS I 313 " --> pdb=" O GLU I 309 " (cutoff:3.500A) Proline residue: I 316 - end of helix removed outlier: 3.505A pdb=" N PHE I 321 " --> pdb=" O PHE I 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 333 removed outlier: 3.831A pdb=" N SER I 333 " --> pdb=" O GLU I 329 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 372 removed outlier: 3.547A pdb=" N GLU I 350 " --> pdb=" O SER I 346 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA I 353 " --> pdb=" O LYS I 349 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA I 372 " --> pdb=" O LEU I 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 436 through 451 Processing helix chain 'I' and resid 469 through 479 removed outlier: 4.101A pdb=" N ILE I 477 " --> pdb=" O GLU I 473 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU I 478 " --> pdb=" O ALA I 474 " (cutoff:3.500A) Processing helix chain 'I' and resid 482 through 486 removed outlier: 3.586A pdb=" N ARG I 485 " --> pdb=" O GLN I 482 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP I 486 " --> pdb=" O VAL I 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 482 through 486' Processing helix chain 'I' and resid 509 through 515 removed outlier: 4.053A pdb=" N PHE I 513 " --> pdb=" O ASN I 509 " (cutoff:3.500A) Processing helix chain 'I' and resid 515 through 521 Processing helix chain 'I' and resid 537 through 542 removed outlier: 3.567A pdb=" N TYR I 541 " --> pdb=" O ARG I 537 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY I 542 " --> pdb=" O GLN I 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 537 through 542' Processing helix chain 'I' and resid 611 through 619 Processing helix chain 'I' and resid 621 through 628 removed outlier: 3.585A pdb=" N ILE I 625 " --> pdb=" O SER I 621 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR I 628 " --> pdb=" O PHE I 624 " (cutoff:3.500A) Processing helix chain 'I' and resid 640 through 651 removed outlier: 3.567A pdb=" N LEU I 644 " --> pdb=" O ASN I 640 " (cutoff:3.500A) Processing helix chain 'I' and resid 674 through 685 removed outlier: 3.951A pdb=" N LEU I 678 " --> pdb=" O THR I 674 " (cutoff:3.500A) Processing helix chain 'I' and resid 707 through 727 removed outlier: 3.528A pdb=" N PHE I 727 " --> pdb=" O VAL I 723 " (cutoff:3.500A) Processing helix chain 'I' and resid 746 through 756 Processing helix chain 'I' and resid 759 through 776 removed outlier: 3.583A pdb=" N LEU I 763 " --> pdb=" O THR I 759 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE I 769 " --> pdb=" O ALA I 765 " (cutoff:3.500A) Proline residue: I 770 - end of helix Processing helix chain 'I' and resid 787 through 811 removed outlier: 3.533A pdb=" N PHE I 796 " --> pdb=" O PHE I 792 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE I 799 " --> pdb=" O LEU I 795 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE I 800 " --> pdb=" O PHE I 796 " (cutoff:3.500A) Processing helix chain 'I' and resid 813 through 846 removed outlier: 3.506A pdb=" N ILE I 826 " --> pdb=" O GLN I 822 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER I 830 " --> pdb=" O ILE I 826 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS I 832 " --> pdb=" O GLY I 828 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU I 833 " --> pdb=" O VAL I 829 " (cutoff:3.500A) Processing helix chain 'I' and resid 870 through 875 removed outlier: 3.847A pdb=" N LEU I 875 " --> pdb=" O TRP I 871 " (cutoff:3.500A) Processing helix chain 'I' and resid 875 through 899 removed outlier: 3.618A pdb=" N ALA I 891 " --> pdb=" O VAL I 887 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE I 893 " --> pdb=" O VAL I 889 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER I 894 " --> pdb=" O VAL I 890 " (cutoff:3.500A) Processing helix chain 'I' and resid 905 through 922 removed outlier: 3.619A pdb=" N VAL I 917 " --> pdb=" O PHE I 913 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS I 920 " --> pdb=" O TRP I 916 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU I 921 " --> pdb=" O VAL I 917 " (cutoff:3.500A) Processing helix chain 'I' and resid 926 through 930 Processing helix chain 'I' and resid 935 through 954 removed outlier: 4.345A pdb=" N VAL I 939 " --> pdb=" O THR I 935 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR I 947 " --> pdb=" O SER I 943 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER I 948 " --> pdb=" O VAL I 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 194 removed outlier: 3.621A pdb=" N ILE C 177 " --> pdb=" O TYR C 173 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE C 182 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN C 194 " --> pdb=" O TYR C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 222 removed outlier: 3.507A pdb=" N TRP C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 234 through 242 Processing helix chain 'C' and resid 266 through 279 removed outlier: 4.271A pdb=" N THR C 270 " --> pdb=" O PRO C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 322 removed outlier: 3.632A pdb=" N PHE C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Proline residue: C 316 - end of helix Processing helix chain 'C' and resid 327 through 333 removed outlier: 3.784A pdb=" N SER C 333 " --> pdb=" O GLU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 372 removed outlier: 3.730A pdb=" N GLU C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 451 Processing helix chain 'C' and resid 469 through 479 removed outlier: 4.102A pdb=" N ILE C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 486 removed outlier: 4.242A pdb=" N ASP C 486 " --> pdb=" O VAL C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 515 removed outlier: 4.069A pdb=" N PHE C 513 " --> pdb=" O ASN C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 521 Processing helix chain 'C' and resid 537 through 542 removed outlier: 3.516A pdb=" N TYR C 541 " --> pdb=" O ARG C 537 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY C 542 " --> pdb=" O GLN C 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 537 through 542' Processing helix chain 'C' and resid 611 through 618 Processing helix chain 'C' and resid 621 through 628 removed outlier: 3.537A pdb=" N ILE C 625 " --> pdb=" O SER C 621 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR C 628 " --> pdb=" O PHE C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 651 removed outlier: 3.536A pdb=" N LEU C 644 " --> pdb=" O ASN C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 685 removed outlier: 4.122A pdb=" N LEU C 678 " --> pdb=" O THR C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 727 removed outlier: 3.519A pdb=" N PHE C 727 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 756 Processing helix chain 'C' and resid 759 through 776 removed outlier: 3.595A pdb=" N LEU C 763 " --> pdb=" O THR C 759 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE C 769 " --> pdb=" O ALA C 765 " (cutoff:3.500A) Proline residue: C 770 - end of helix Processing helix chain 'C' and resid 787 through 811 removed outlier: 3.837A pdb=" N LEU C 791 " --> pdb=" O LEU C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 846 removed outlier: 3.737A pdb=" N ILE C 826 " --> pdb=" O GLN C 822 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 830 " --> pdb=" O ILE C 826 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N HIS C 832 " --> pdb=" O GLY C 828 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU C 833 " --> pdb=" O VAL C 829 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE C 834 " --> pdb=" O SER C 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 875 removed outlier: 3.766A pdb=" N LEU C 875 " --> pdb=" O TRP C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 875 through 899 removed outlier: 3.926A pdb=" N THR C 879 " --> pdb=" O LEU C 875 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR C 880 " --> pdb=" O ILE C 876 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN C 885 " --> pdb=" O LEU C 881 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 890 " --> pdb=" O ILE C 886 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA C 891 " --> pdb=" O VAL C 887 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE C 893 " --> pdb=" O VAL C 889 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER C 894 " --> pdb=" O VAL C 890 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 928 removed outlier: 3.570A pdb=" N HIS C 920 " --> pdb=" O TRP C 916 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 921 " --> pdb=" O VAL C 917 " (cutoff:3.500A) Proline residue: C 923 - end of helix removed outlier: 4.220A pdb=" N LEU C 928 " --> pdb=" O PHE C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 934 through 955 removed outlier: 5.612A pdb=" N VAL C 940 " --> pdb=" O PRO C 936 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 160 through 164 Processing sheet with id=AA2, first strand: chain 'D' and resid 399 through 403 removed outlier: 6.843A pdb=" N CYS D 289 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL D 423 " --> pdb=" O CYS D 289 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL D 291 " --> pdb=" O VAL D 423 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE D 255 " --> pdb=" O TYR D 290 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N SER D 292 " --> pdb=" O PHE D 255 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL D 257 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ASP D 254 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N CYS D 533 " --> pdb=" O ASN D 458 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL D 534 " --> pdb=" O VAL D 490 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 490 " --> pdb=" O VAL D 534 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 495 through 496 removed outlier: 7.438A pdb=" N ARG D 495 " --> pdb=" O GLY D 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'I' and resid 160 through 164 Processing sheet with id=AA5, first strand: chain 'I' and resid 399 through 403 removed outlier: 6.837A pdb=" N CYS I 289 " --> pdb=" O VAL I 421 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N VAL I 423 " --> pdb=" O CYS I 289 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL I 291 " --> pdb=" O VAL I 423 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE I 255 " --> pdb=" O TYR I 290 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N SER I 292 " --> pdb=" O PHE I 255 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL I 257 " --> pdb=" O SER I 292 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASP I 254 " --> pdb=" O LEU I 457 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N CYS I 533 " --> pdb=" O ASN I 458 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL I 534 " --> pdb=" O VAL I 490 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL I 490 " --> pdb=" O VAL I 534 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 160 through 164 Processing sheet with id=AA7, first strand: chain 'C' and resid 399 through 403 removed outlier: 6.643A pdb=" N CYS C 289 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL C 423 " --> pdb=" O CYS C 289 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL C 291 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASP C 254 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN C 458 " --> pdb=" O CYS C 533 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N CYS C 533 " --> pdb=" O ASN C 458 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C 534 " --> pdb=" O VAL C 490 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 490 " --> pdb=" O VAL C 534 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 495 through 496 removed outlier: 7.476A pdb=" N ARG C 495 " --> pdb=" O GLY C 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 812 hydrogen bonds defined for protein. 2418 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: 12.33 Time building geometry restraints manager: 10.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 16846 1.03 - 1.23: 42 1.23 - 1.42: 7627 1.42 - 1.62: 10255 1.62 - 1.81: 135 Bond restraints: 34905 Sorted by residual: bond pdb=" O1A UDP D1001 " pdb=" PA UDP D1001 " ideal model delta sigma weight residual 1.482 1.526 -0.044 1.00e-02 1.00e+04 1.96e+01 bond pdb=" O1B UDP I1001 " pdb=" PB UDP I1001 " ideal model delta sigma weight residual 1.530 1.495 0.035 1.00e-02 1.00e+04 1.25e+01 bond pdb=" C1 BGC A 2 " pdb=" O5 BGC A 2 " ideal model delta sigma weight residual 1.408 1.466 -0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" O2A UDP D1001 " pdb=" PA UDP D1001 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.80e-02 3.09e+03 6.16e+00 bond pdb=" C1 BGC B 3 " pdb=" O5 BGC B 3 " ideal model delta sigma weight residual 1.408 1.458 -0.050 2.00e-02 2.50e+03 6.13e+00 ... (remaining 34900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.28: 62777 7.28 - 14.55: 10 14.55 - 21.83: 0 21.83 - 29.10: 21 29.10 - 36.38: 66 Bond angle restraints: 62874 Sorted by residual: angle pdb=" C SER C 638 " pdb=" CA SER C 638 " pdb=" HA SER C 638 " ideal model delta sigma weight residual 109.00 72.62 36.38 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C THR D 937 " pdb=" CA THR D 937 " pdb=" HA THR D 937 " ideal model delta sigma weight residual 109.00 72.66 36.34 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C SER I 638 " pdb=" CA SER I 638 " pdb=" HA SER I 638 " ideal model delta sigma weight residual 109.00 72.67 36.33 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C ALA D 639 " pdb=" CA ALA D 639 " pdb=" HA ALA D 639 " ideal model delta sigma weight residual 109.00 73.14 35.86 3.00e+00 1.11e-01 1.43e+02 angle pdb=" C ALA I 639 " pdb=" CA ALA I 639 " pdb=" HA ALA I 639 " ideal model delta sigma weight residual 109.00 73.22 35.78 3.00e+00 1.11e-01 1.42e+02 ... (remaining 62869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.20: 15793 26.20 - 52.40: 882 52.40 - 78.59: 140 78.59 - 104.79: 22 104.79 - 130.99: 13 Dihedral angle restraints: 16850 sinusoidal: 9152 harmonic: 7698 Sorted by residual: dihedral pdb=" CA GLY I 905 " pdb=" C GLY I 905 " pdb=" N PRO I 906 " pdb=" CA PRO I 906 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" C THR D 937 " pdb=" N THR D 937 " pdb=" CA THR D 937 " pdb=" CB THR D 937 " ideal model delta harmonic sigma weight residual -122.00 -133.63 11.63 0 2.50e+00 1.60e-01 2.16e+01 dihedral pdb=" CA GLY C 905 " pdb=" C GLY C 905 " pdb=" N PRO C 906 " pdb=" CA PRO C 906 " ideal model delta harmonic sigma weight residual 180.00 157.39 22.61 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 16847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.290: 2706 0.290 - 0.579: 20 0.579 - 0.869: 0 0.869 - 1.158: 0 1.158 - 1.448: 3 Chirality restraints: 2729 Sorted by residual: chirality pdb=" CB THR C 872 " pdb=" CA THR C 872 " pdb=" OG1 THR C 872 " pdb=" CG2 THR C 872 " both_signs ideal model delta sigma weight residual False 2.55 1.10 1.45 2.00e-01 2.50e+01 5.24e+01 chirality pdb=" CB THR I 872 " pdb=" CA THR I 872 " pdb=" OG1 THR I 872 " pdb=" CG2 THR I 872 " both_signs ideal model delta sigma weight residual False 2.55 1.11 1.44 2.00e-01 2.50e+01 5.20e+01 chirality pdb=" CB THR D 872 " pdb=" CA THR D 872 " pdb=" OG1 THR D 872 " pdb=" CG2 THR D 872 " both_signs ideal model delta sigma weight residual False 2.55 1.14 1.41 2.00e-01 2.50e+01 4.96e+01 ... (remaining 2726 not shown) Planarity restraints: 5058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 761 " 0.052 5.00e-02 4.00e+02 7.83e-02 9.82e+00 pdb=" N PRO D 762 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 762 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 762 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 222 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.79e+00 pdb=" N PRO C 223 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 223 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 223 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 796 " -0.019 2.00e-02 2.50e+03 1.36e-02 5.54e+00 pdb=" CG PHE I 796 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE I 796 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE I 796 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE I 796 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE I 796 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE I 796 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE I 796 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE I 796 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE I 796 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 PHE I 796 " -0.008 2.00e-02 2.50e+03 pdb=" HZ PHE I 796 " 0.001 2.00e-02 2.50e+03 ... (remaining 5055 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 604 2.12 - 2.74: 56889 2.74 - 3.36: 90116 3.36 - 3.98: 105934 3.98 - 4.60: 169622 Nonbonded interactions: 423165 Sorted by model distance: nonbonded pdb="MG MG I1002 " pdb="MG MG I1003 " model vdw 1.501 1.300 nonbonded pdb="MG MG C1002 " pdb="MG MG C1003 " model vdw 1.517 1.300 nonbonded pdb="MG MG D1002 " pdb="MG MG D1003 " model vdw 1.527 1.300 nonbonded pdb=" H TRP D 904 " pdb=" HA TRP D 904 " model vdw 1.581 1.816 nonbonded pdb=" H LEU C 921 " pdb=" HA LEU C 921 " model vdw 1.582 1.816 ... (remaining 423160 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' selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 157 through 954 or resid 1001 or resid 1002 through 1003)) \ selection = chain 'D' selection = (chain 'I' and (resid 157 through 954 or resid 1001 or resid 1002 through 1003)) \ } 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: 5.530 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: 0.670 Extract box with map and model: 1.460 Check model and map are aligned: 0.260 Set scattering table: 0.350 Process input model: 72.410 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.110 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.864 18033 Z= 0.658 Angle : 0.590 11.517 24565 Z= 0.306 Chirality : 0.068 1.448 2729 Planarity : 0.004 0.078 3051 Dihedral : 16.756 130.990 6792 Min Nonbonded Distance : 1.501 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.19 % Favored : 94.62 % Rotamer: Outliers : 0.05 % Allowed : 10.68 % Favored : 89.26 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 4.55 % 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 (0.19), residues: 2139 helix: 2.24 (0.17), residues: 1053 sheet: 0.10 (0.43), residues: 136 loop : -1.48 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 916 HIS 0.001 0.000 HIS D 920 PHE 0.040 0.001 PHE I 796 TYR 0.010 0.001 TYR C 756 ARG 0.007 0.000 ARG C 931 Details of bonding type rmsd link_BETA1-4 : bond 0.00625 ( 12) link_BETA1-4 : angle 1.49485 ( 36) hydrogen bonds : bond 0.23776 ( 812) hydrogen bonds : angle 6.21003 ( 2418) covalent geometry : bond 0.00287 (18020) covalent geometry : angle 0.58790 (24529) Misc. bond : bond 0.86405 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 212 TRP cc_start: 0.8346 (t-100) cc_final: 0.7887 (t-100) REVERT: D 758 PHE cc_start: 0.7365 (m-10) cc_final: 0.6847 (m-10) REVERT: I 837 PHE cc_start: 0.7935 (t80) cc_final: 0.7479 (t80) outliers start: 1 outliers final: 1 residues processed: 209 average time/residue: 0.6387 time to fit residues: 204.0115 Evaluate side-chains 202 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 799 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 714 GLN D 920 HIS C 509 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.135340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.097516 restraints weight = 92440.363| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.86 r_work: 0.3249 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18033 Z= 0.179 Angle : 0.687 11.470 24565 Z= 0.358 Chirality : 0.071 1.435 2729 Planarity : 0.005 0.054 3051 Dihedral : 11.070 112.790 2741 Min Nonbonded Distance : 1.204 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.14 % Favored : 94.67 % Rotamer: Outliers : 1.18 % Allowed : 10.52 % Favored : 88.30 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 2139 helix: 1.99 (0.16), residues: 1078 sheet: 0.05 (0.45), residues: 131 loop : -1.51 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 203 HIS 0.005 0.001 HIS I 434 PHE 0.021 0.001 PHE I 913 TYR 0.013 0.001 TYR C 756 ARG 0.005 0.000 ARG C 445 Details of bonding type rmsd link_BETA1-4 : bond 0.00543 ( 12) link_BETA1-4 : angle 2.15864 ( 36) hydrogen bonds : bond 0.08362 ( 812) hydrogen bonds : angle 4.73485 ( 2418) covalent geometry : bond 0.00384 (18020) covalent geometry : angle 0.68259 (24529) Misc. bond : bond 0.01798 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 2.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 218 average time/residue: 0.6805 time to fit residues: 224.4534 Evaluate side-chains 202 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 709 SER Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 694 MET Chi-restraints excluded: chain I residue 790 MET Chi-restraints excluded: chain I residue 800 ILE Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 952 LEU Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 883 ILE Chi-restraints excluded: chain C residue 919 LEU Chi-restraints excluded: chain C residue 950 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 chunk 165 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 110 optimal weight: 0.1980 chunk 119 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 524 GLN D 920 HIS I 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.134539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.100909 restraints weight = 92947.849| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.33 r_work: 0.3189 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18033 Z= 0.146 Angle : 0.626 11.513 24565 Z= 0.320 Chirality : 0.070 1.442 2729 Planarity : 0.005 0.137 3051 Dihedral : 10.325 105.977 2741 Min Nonbonded Distance : 1.101 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.28 % Favored : 94.53 % Rotamer: Outliers : 1.02 % Allowed : 11.49 % Favored : 87.49 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2139 helix: 2.03 (0.16), residues: 1075 sheet: -0.00 (0.45), residues: 131 loop : -1.51 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 954 HIS 0.005 0.001 HIS I 434 PHE 0.012 0.001 PHE I 796 TYR 0.013 0.001 TYR C 756 ARG 0.027 0.000 ARG D 717 Details of bonding type rmsd link_BETA1-4 : bond 0.00402 ( 12) link_BETA1-4 : angle 1.86910 ( 36) hydrogen bonds : bond 0.07684 ( 812) hydrogen bonds : angle 4.44765 ( 2418) covalent geometry : bond 0.00309 (18020) covalent geometry : angle 0.62220 (24529) Misc. bond : bond 0.00166 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 797 ILE cc_start: 0.9118 (tt) cc_final: 0.8902 (mt) REVERT: I 837 PHE cc_start: 0.8177 (t80) cc_final: 0.7692 (t80) REVERT: C 926 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8101 (tptt) outliers start: 19 outliers final: 15 residues processed: 212 average time/residue: 0.6775 time to fit residues: 222.2725 Evaluate side-chains 205 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 615 GLU Chi-restraints excluded: chain I residue 694 MET Chi-restraints excluded: chain I residue 756 TYR Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain I residue 790 MET Chi-restraints excluded: chain I residue 800 ILE Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 952 LEU Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 926 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.130791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.092220 restraints weight = 92858.917| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.81 r_work: 0.3147 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.179 18033 Z= 0.190 Angle : 0.665 11.546 24565 Z= 0.341 Chirality : 0.071 1.460 2729 Planarity : 0.006 0.203 3051 Dihedral : 8.869 92.752 2741 Min Nonbonded Distance : 1.071 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.89 % Favored : 93.92 % Rotamer: Outliers : 1.07 % Allowed : 12.24 % Favored : 86.69 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 4.55 % 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: 0.38 (0.18), residues: 2139 helix: 1.84 (0.16), residues: 1074 sheet: -0.33 (0.44), residues: 131 loop : -1.65 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 954 HIS 0.007 0.001 HIS I 434 PHE 0.018 0.001 PHE I 913 TYR 0.034 0.002 TYR D 505 ARG 0.036 0.001 ARG D 717 Details of bonding type rmsd link_BETA1-4 : bond 0.00349 ( 12) link_BETA1-4 : angle 2.30401 ( 36) hydrogen bonds : bond 0.07138 ( 812) hydrogen bonds : angle 4.35666 ( 2418) covalent geometry : bond 0.00440 (18020) covalent geometry : angle 0.65964 (24529) Misc. bond : bond 0.02323 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 786 ASN cc_start: 0.7814 (t0) cc_final: 0.7408 (t0) REVERT: C 926 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8128 (tptt) outliers start: 20 outliers final: 17 residues processed: 210 average time/residue: 0.6930 time to fit residues: 224.9971 Evaluate side-chains 210 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 615 GLU Chi-restraints excluded: chain I residue 694 MET Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain I residue 790 MET Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 952 LEU Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 893 PHE Chi-restraints excluded: chain C residue 926 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 51 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.131575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.096703 restraints weight = 92950.956| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.37 r_work: 0.3136 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18033 Z= 0.132 Angle : 0.612 11.572 24565 Z= 0.311 Chirality : 0.069 1.460 2729 Planarity : 0.005 0.053 3051 Dihedral : 7.605 75.151 2741 Min Nonbonded Distance : 1.155 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.24 % Favored : 94.58 % Rotamer: Outliers : 1.23 % Allowed : 12.94 % Favored : 85.83 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 4.55 % 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: 0.66 (0.18), residues: 2139 helix: 2.15 (0.16), residues: 1070 sheet: -0.39 (0.44), residues: 131 loop : -1.58 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 809 HIS 0.003 0.001 HIS I 434 PHE 0.011 0.001 PHE D 317 TYR 0.014 0.001 TYR C 190 ARG 0.023 0.000 ARG D 717 Details of bonding type rmsd link_BETA1-4 : bond 0.00286 ( 12) link_BETA1-4 : angle 2.17102 ( 36) hydrogen bonds : bond 0.06290 ( 812) hydrogen bonds : angle 4.12450 ( 2418) covalent geometry : bond 0.00288 (18020) covalent geometry : angle 0.60654 (24529) Misc. bond : bond 0.01188 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 630 MET cc_start: 0.7811 (mmm) cc_final: 0.7574 (mmm) REVERT: I 786 ASN cc_start: 0.7831 (t0) cc_final: 0.7379 (t0) REVERT: I 941 LEU cc_start: 0.8756 (tp) cc_final: 0.8515 (tt) REVERT: C 926 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8063 (tptt) outliers start: 23 outliers final: 17 residues processed: 217 average time/residue: 0.6215 time to fit residues: 205.2617 Evaluate side-chains 211 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain D residue 929 MET Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 615 GLU Chi-restraints excluded: chain I residue 694 MET Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain I residue 790 MET Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 952 LEU Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 893 PHE Chi-restraints excluded: chain C residue 926 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 188 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.131900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.097394 restraints weight = 92273.118| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.27 r_work: 0.3140 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18033 Z= 0.124 Angle : 0.586 11.560 24565 Z= 0.302 Chirality : 0.069 1.453 2729 Planarity : 0.005 0.164 3051 Dihedral : 6.217 72.342 2741 Min Nonbonded Distance : 1.154 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.42 % Favored : 94.34 % Rotamer: Outliers : 1.02 % Allowed : 13.53 % Favored : 85.45 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.18), residues: 2139 helix: 2.33 (0.16), residues: 1055 sheet: -0.38 (0.44), residues: 131 loop : -1.56 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 809 HIS 0.003 0.001 HIS D 920 PHE 0.028 0.001 PHE I 913 TYR 0.014 0.001 TYR I 505 ARG 0.026 0.000 ARG D 717 Details of bonding type rmsd link_BETA1-4 : bond 0.00406 ( 12) link_BETA1-4 : angle 1.85082 ( 36) hydrogen bonds : bond 0.05641 ( 812) hydrogen bonds : angle 3.98291 ( 2418) covalent geometry : bond 0.00273 (18020) covalent geometry : angle 0.58179 (24529) Misc. bond : bond 0.00183 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 204 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 527 MET cc_start: 0.7115 (OUTLIER) cc_final: 0.6574 (mmt) REVERT: I 786 ASN cc_start: 0.7800 (t0) cc_final: 0.7303 (t0) REVERT: I 941 LEU cc_start: 0.8604 (tp) cc_final: 0.8341 (tt) REVERT: C 926 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8013 (tptt) outliers start: 19 outliers final: 16 residues processed: 214 average time/residue: 0.6304 time to fit residues: 208.0520 Evaluate side-chains 212 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 416 GLU Chi-restraints excluded: chain I residue 615 GLU Chi-restraints excluded: chain I residue 694 MET Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain I residue 790 MET Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 951 SER Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 893 PHE Chi-restraints excluded: chain C residue 926 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 164 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 150 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 509 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.132669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.094342 restraints weight = 92565.048| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.84 r_work: 0.3180 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 18033 Z= 0.114 Angle : 0.561 11.506 24565 Z= 0.291 Chirality : 0.069 1.444 2729 Planarity : 0.006 0.193 3051 Dihedral : 5.874 73.575 2741 Min Nonbonded Distance : 1.169 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.86 % Favored : 94.90 % Rotamer: Outliers : 1.02 % Allowed : 13.74 % Favored : 85.24 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 4.55 % 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: 0.90 (0.19), residues: 2139 helix: 2.47 (0.16), residues: 1054 sheet: -0.35 (0.44), residues: 131 loop : -1.54 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 809 HIS 0.002 0.001 HIS I 434 PHE 0.010 0.001 PHE D 317 TYR 0.012 0.001 TYR D 750 ARG 0.021 0.000 ARG D 717 Details of bonding type rmsd link_BETA1-4 : bond 0.00286 ( 12) link_BETA1-4 : angle 1.22867 ( 36) hydrogen bonds : bond 0.05213 ( 812) hydrogen bonds : angle 3.86728 ( 2418) covalent geometry : bond 0.00247 (18020) covalent geometry : angle 0.55946 (24529) Misc. bond : bond 0.00947 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 786 ASN cc_start: 0.7914 (t0) cc_final: 0.7643 (t0) REVERT: I 941 LEU cc_start: 0.8542 (tp) cc_final: 0.8262 (tt) REVERT: C 926 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8006 (tptt) outliers start: 19 outliers final: 16 residues processed: 212 average time/residue: 0.6289 time to fit residues: 205.4418 Evaluate side-chains 212 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 336 ILE Chi-restraints excluded: chain I residue 615 GLU Chi-restraints excluded: chain I residue 694 MET Chi-restraints excluded: chain I residue 772 VAL Chi-restraints excluded: chain I residue 790 MET Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 893 PHE Chi-restraints excluded: chain C residue 926 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 114 optimal weight: 2.9990 chunk 182 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 197 optimal weight: 0.6980 chunk 211 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.132278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.097428 restraints weight = 92182.553| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.24 r_work: 0.3146 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 18033 Z= 0.116 Angle : 0.557 11.503 24565 Z= 0.289 Chirality : 0.069 1.444 2729 Planarity : 0.005 0.162 3051 Dihedral : 5.710 88.840 2741 Min Nonbonded Distance : 1.157 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.05 % Favored : 94.72 % Rotamer: Outliers : 1.07 % Allowed : 14.12 % Favored : 84.81 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 4.55 % 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 (0.19), residues: 2139 helix: 2.53 (0.16), residues: 1053 sheet: -0.36 (0.44), residues: 130 loop : -1.55 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 809 HIS 0.003 0.001 HIS I 434 PHE 0.024 0.001 PHE I 913 TYR 0.015 0.001 TYR D 750 ARG 0.020 0.000 ARG D 717 Details of bonding type rmsd link_BETA1-4 : bond 0.00245 ( 12) link_BETA1-4 : angle 1.24010 ( 36) hydrogen bonds : bond 0.05029 ( 812) hydrogen bonds : angle 3.81862 ( 2418) covalent geometry : bond 0.00261 (18020) covalent geometry : angle 0.55496 (24529) Misc. bond : bond 0.00537 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 527 MET cc_start: 0.6909 (mmt) cc_final: 0.6170 (mmt) REVERT: D 630 MET cc_start: 0.7954 (mmm) cc_final: 0.7648 (mmm) REVERT: I 473 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7756 (mt-10) REVERT: I 786 ASN cc_start: 0.7921 (t0) cc_final: 0.7644 (t0) REVERT: I 941 LEU cc_start: 0.8534 (tp) cc_final: 0.8270 (tt) REVERT: I 951 SER cc_start: 0.8821 (OUTLIER) cc_final: 0.8379 (p) REVERT: C 210 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8836 (mm-30) REVERT: C 926 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7970 (tptt) outliers start: 20 outliers final: 15 residues processed: 209 average time/residue: 0.6124 time to fit residues: 197.9010 Evaluate side-chains 213 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain D residue 929 MET Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 336 ILE Chi-restraints excluded: chain I residue 615 GLU Chi-restraints excluded: chain I residue 694 MET Chi-restraints excluded: chain I residue 790 MET Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 951 SER Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 893 PHE Chi-restraints excluded: chain C residue 926 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 127 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.130368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.091646 restraints weight = 92164.502| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.83 r_work: 0.3147 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 18033 Z= 0.145 Angle : 0.580 11.518 24565 Z= 0.303 Chirality : 0.069 1.442 2729 Planarity : 0.006 0.183 3051 Dihedral : 5.497 73.895 2741 Min Nonbonded Distance : 1.117 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.47 % Favored : 94.30 % Rotamer: Outliers : 0.86 % Allowed : 14.28 % Favored : 84.86 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 4.55 % 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: 0.79 (0.18), residues: 2139 helix: 2.43 (0.16), residues: 1054 sheet: -0.49 (0.44), residues: 130 loop : -1.64 (0.18), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 809 HIS 0.005 0.001 HIS I 434 PHE 0.014 0.001 PHE D 317 TYR 0.016 0.001 TYR I 505 ARG 0.023 0.000 ARG D 717 Details of bonding type rmsd link_BETA1-4 : bond 0.00197 ( 12) link_BETA1-4 : angle 1.41232 ( 36) hydrogen bonds : bond 0.05655 ( 812) hydrogen bonds : angle 3.91429 ( 2418) covalent geometry : bond 0.00340 (18020) covalent geometry : angle 0.57784 (24529) Misc. bond : bond 0.00686 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 2.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 630 MET cc_start: 0.7926 (mmm) cc_final: 0.7622 (mmm) REVERT: I 473 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8052 (mt-10) REVERT: I 503 ASP cc_start: 0.7260 (t0) cc_final: 0.7048 (t0) REVERT: I 941 LEU cc_start: 0.8526 (tp) cc_final: 0.8237 (tt) REVERT: I 951 SER cc_start: 0.8833 (OUTLIER) cc_final: 0.8403 (p) REVERT: C 210 GLU cc_start: 0.9223 (mm-30) cc_final: 0.9001 (mm-30) REVERT: C 926 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8025 (tptt) outliers start: 16 outliers final: 13 residues processed: 216 average time/residue: 0.6511 time to fit residues: 218.5460 Evaluate side-chains 215 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 200 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 615 GLU Chi-restraints excluded: chain I residue 694 MET Chi-restraints excluded: chain I residue 790 MET Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 951 SER Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 893 PHE Chi-restraints excluded: chain C residue 926 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 174 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 152 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 191 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.131525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.093690 restraints weight = 91655.983| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.72 r_work: 0.3171 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18033 Z= 0.115 Angle : 0.562 11.531 24565 Z= 0.293 Chirality : 0.069 1.446 2729 Planarity : 0.005 0.126 3051 Dihedral : 5.340 68.290 2741 Min Nonbonded Distance : 1.169 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.96 % Favored : 94.81 % Rotamer: Outliers : 0.86 % Allowed : 14.55 % Favored : 84.59 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 4.55 % 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: 0.90 (0.19), residues: 2139 helix: 2.54 (0.16), residues: 1054 sheet: -0.44 (0.44), residues: 130 loop : -1.61 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 809 HIS 0.003 0.001 HIS D 920 PHE 0.022 0.001 PHE I 913 TYR 0.012 0.001 TYR C 756 ARG 0.019 0.000 ARG D 717 Details of bonding type rmsd link_BETA1-4 : bond 0.00230 ( 12) link_BETA1-4 : angle 1.21490 ( 36) hydrogen bonds : bond 0.05156 ( 812) hydrogen bonds : angle 3.81606 ( 2418) covalent geometry : bond 0.00256 (18020) covalent geometry : angle 0.56056 (24529) Misc. bond : bond 0.00486 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4278 Ramachandran restraints generated. 2139 Oldfield, 0 Emsley, 2139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 527 MET cc_start: 0.7488 (mmt) cc_final: 0.6814 (mmt) REVERT: D 630 MET cc_start: 0.7953 (mmm) cc_final: 0.7669 (mmm) REVERT: I 473 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7995 (mt-10) REVERT: I 941 LEU cc_start: 0.8518 (tp) cc_final: 0.8217 (tt) REVERT: I 951 SER cc_start: 0.8781 (OUTLIER) cc_final: 0.8382 (p) REVERT: C 926 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8006 (tptt) outliers start: 16 outliers final: 12 residues processed: 213 average time/residue: 0.6263 time to fit residues: 206.3123 Evaluate side-chains 214 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 3.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain I residue 318 CYS Chi-restraints excluded: chain I residue 615 GLU Chi-restraints excluded: chain I residue 694 MET Chi-restraints excluded: chain I residue 935 THR Chi-restraints excluded: chain I residue 951 SER Chi-restraints excluded: chain C residue 163 TYR Chi-restraints excluded: chain C residue 780 ILE Chi-restraints excluded: chain C residue 799 ILE Chi-restraints excluded: chain C residue 820 ASN Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 893 PHE Chi-restraints excluded: chain C residue 926 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 117 optimal weight: 1.9990 chunk 169 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 131 optimal weight: 0.2980 chunk 124 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.131673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.094165 restraints weight = 91197.720| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.71 r_work: 0.3174 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18033 Z= 0.118 Angle : 0.568 11.504 24565 Z= 0.295 Chirality : 0.069 1.439 2729 Planarity : 0.005 0.144 3051 Dihedral : 5.278 67.888 2741 Min Nonbonded Distance : 1.160 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.38 % Favored : 94.39 % Rotamer: Outliers : 0.75 % Allowed : 14.76 % Favored : 84.49 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 4.55 % 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: 0.91 (0.19), residues: 2139 helix: 2.54 (0.16), residues: 1054 sheet: -0.44 (0.44), residues: 130 loop : -1.60 (0.19), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 809 HIS 0.006 0.001 HIS D 920 PHE 0.011 0.001 PHE D 317 TYR 0.012 0.001 TYR C 756 ARG 0.022 0.000 ARG D 717 Details of bonding type rmsd link_BETA1-4 : bond 0.00211 ( 12) link_BETA1-4 : angle 1.22224 ( 36) hydrogen bonds : bond 0.05059 ( 812) hydrogen bonds : angle 3.79090 ( 2418) covalent geometry : bond 0.00266 (18020) covalent geometry : angle 0.56654 (24529) Misc. bond : bond 0.00497 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16105.73 seconds wall clock time: 273 minutes 35.76 seconds (16415.76 seconds total)