Starting phenix.real_space_refine on Sat Aug 23 16:06:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t8m_41099/08_2025/8t8m_41099.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t8m_41099/08_2025/8t8m_41099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t8m_41099/08_2025/8t8m_41099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t8m_41099/08_2025/8t8m_41099.map" model { file = "/net/cci-nas-00/data/ceres_data/8t8m_41099/08_2025/8t8m_41099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t8m_41099/08_2025/8t8m_41099.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 Anisotropic ADP refinement not supported. Converting 136 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 8306 2.51 5 N 2254 2.21 5 O 2472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13146 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5590 Classifications: {'peptide': 757} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 725} Chain breaks: 3 Unresolved non-hydrogen bonds: 418 Unresolved non-hydrogen angles: 529 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 9, 'GLN:plan1': 4, 'TYR:plan': 12, 'ASP:plan': 2, 'PHE:plan': 7, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 230 Chain: "B" Number of atoms: 5660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5660 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 416 Unresolved non-hydrogen angles: 529 Unresolved non-hydrogen dihedrals: 353 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 9, 'ARG:plan': 9, 'TYR:plan': 12, 'PHE:plan': 7, 'GLN:plan1': 2, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 233 Chain: "C" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 939 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Chain: "D" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 931 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.98, per 1000 atoms: 0.23 Number of scatterers: 13146 At special positions: 0 Unit cell: (109.989, 83.325, 206.646, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 2472 8.00 N 2254 7.00 C 8306 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 530 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 98 " distance=2.04 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 98 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 647.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3284 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 18 sheets defined 42.0% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 64 through 80 Processing helix chain 'A' and resid 101 through 113 removed outlier: 3.817A pdb=" N GLU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 163 Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.684A pdb=" N ASP A 181 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 208 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.901A pdb=" N LYS A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 265 removed outlier: 3.504A pdb=" N PHE A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 279 through 293 Processing helix chain 'A' and resid 334 through 342 removed outlier: 3.900A pdb=" N ASP A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 396 through 416 Processing helix chain 'A' and resid 433 through 442 Processing helix chain 'A' and resid 577 through 604 Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.542A pdb=" N SER A 612 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 637 removed outlier: 4.503A pdb=" N ILE A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ALA A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 669 Proline residue: A 655 - end of helix removed outlier: 3.768A pdb=" N ILE A 669 " --> pdb=" O LYS A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 715 removed outlier: 3.611A pdb=" N ILE A 696 " --> pdb=" O ALA A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 761 Processing helix chain 'A' and resid 769 through 793 removed outlier: 3.770A pdb=" N TYR A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) Proline residue: A 790 - end of helix removed outlier: 4.046A pdb=" N PHE A 793 " --> pdb=" O VAL A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 826 Proline residue: A 820 - end of helix Processing helix chain 'B' and resid 66 through 81 removed outlier: 3.520A pdb=" N SER B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 115 Processing helix chain 'B' and resid 151 through 165 removed outlier: 3.553A pdb=" N ASN B 160 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 209 removed outlier: 3.552A pdb=" N TYR B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 239 Processing helix chain 'B' and resid 253 through 266 removed outlier: 3.621A pdb=" N PHE B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 294 Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.846A pdb=" N VAL B 322 " --> pdb=" O ARG B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 342 removed outlier: 4.121A pdb=" N ASP B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 340 " --> pdb=" O TRP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 396 through 419 removed outlier: 3.683A pdb=" N VAL B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 removed outlier: 3.868A pdb=" N LYS B 430 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 Processing helix chain 'B' and resid 495 through 500 removed outlier: 3.645A pdb=" N VAL B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP B 500 " --> pdb=" O ASP B 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 495 through 500' Processing helix chain 'B' and resid 577 through 604 Processing helix chain 'B' and resid 609 through 613 removed outlier: 3.949A pdb=" N SER B 612 " --> pdb=" O VAL B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 634 Processing helix chain 'B' and resid 640 through 669 Proline residue: B 655 - end of helix removed outlier: 3.840A pdb=" N ILE B 669 " --> pdb=" O LYS B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 715 removed outlier: 4.408A pdb=" N LEU B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 761 removed outlier: 3.889A pdb=" N VAL B 741 " --> pdb=" O ASN B 737 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) Proline residue: B 743 - end of helix Processing helix chain 'B' and resid 769 through 793 removed outlier: 3.796A pdb=" N ALA B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE B 776 " --> pdb=" O LYS B 772 " (cutoff:3.500A) Proline residue: B 790 - end of helix removed outlier: 3.914A pdb=" N PHE B 793 " --> pdb=" O VAL B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 826 Proline residue: B 820 - end of helix removed outlier: 3.601A pdb=" N LEU B 826 " --> pdb=" O VAL B 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.967A pdb=" N THR C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 34 removed outlier: 3.630A pdb=" N SER D 33 " --> pdb=" O THR D 30 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR D 34 " --> pdb=" O PHE D 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 30 through 34' Processing helix chain 'D' and resid 64 through 67 removed outlier: 3.616A pdb=" N LYS D 67 " --> pdb=" O ASP D 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 64 through 67' Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.531A pdb=" N THR D 93 " --> pdb=" O PRO D 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 5.955A pdb=" N ILE A 35 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLU A 94 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE A 37 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ARG A 96 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA A 39 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE A 36 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY A 145 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N ILE A 170 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL A 146 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 245 through 248 removed outlier: 6.901A pdb=" N ALA A 216 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ILE A 248 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS A 218 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER A 215 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N PHE A 277 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL A 217 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY A 485 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN A 470 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASN A 483 " --> pdb=" O ASN A 470 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LYS A 472 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N TYR A 481 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 447 Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 524 removed outlier: 3.521A pdb=" N THR A 533 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 541 through 545 removed outlier: 6.623A pdb=" N THR A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 719 through 722 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.650A pdb=" N MET B 31 " --> pdb=" O CYS B 93 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE B 35 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLU B 94 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ARG B 96 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ALA B 39 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE B 36 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY B 145 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N ILE B 170 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL B 146 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 242 through 248 removed outlier: 8.021A pdb=" N VAL B 214 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER B 245 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA B 216 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LYS B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N HIS B 218 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER B 215 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TYR B 466 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER B 486 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE B 468 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 445 through 447 Processing sheet with id=AB1, first strand: chain 'B' and resid 520 through 524 Processing sheet with id=AB2, first strand: chain 'B' and resid 541 through 542 Processing sheet with id=AB3, first strand: chain 'B' and resid 719 through 722 Processing sheet with id=AB4, first strand: chain 'C' and resid 6 through 9 removed outlier: 3.550A pdb=" N LEU C 20 " --> pdb=" O MET C 85 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 13 through 15 removed outlier: 6.894A pdb=" N VAL C 14 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C 51 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ARG C 40 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N SER C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 13 through 15 removed outlier: 6.894A pdb=" N VAL C 14 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR C 114 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 5 through 9 Processing sheet with id=AB8, first strand: chain 'D' and resid 12 through 15 removed outlier: 6.211A pdb=" N GLY D 12 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N SER D 124 " --> pdb=" O GLY D 12 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL D 14 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA D 51 " --> pdb=" O TRP D 38 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ARG D 40 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N SER D 49 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 12 through 15 removed outlier: 6.211A pdb=" N GLY D 12 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N SER D 124 " --> pdb=" O GLY D 12 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL D 14 " --> pdb=" O SER D 124 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA D 100 " --> pdb=" O ASP D 113 " (cutoff:3.500A) 645 hydrogen bonds defined for protein. 1836 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: 2.41 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2189 1.31 - 1.44: 3600 1.44 - 1.56: 7478 1.56 - 1.69: 0 1.69 - 1.82: 162 Bond restraints: 13429 Sorted by residual: bond pdb=" C05 QUS B 901 " pdb=" N15 QUS B 901 " ideal model delta sigma weight residual 1.365 1.441 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C05 QUS A 901 " pdb=" N15 QUS A 901 " ideal model delta sigma weight residual 1.365 1.440 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C05 QUS A 901 " pdb=" O20 QUS A 901 " ideal model delta sigma weight residual 1.362 1.424 -0.062 2.00e-02 2.50e+03 9.52e+00 bond pdb=" C05 QUS B 901 " pdb=" O20 QUS B 901 " ideal model delta sigma weight residual 1.362 1.423 -0.061 2.00e-02 2.50e+03 9.22e+00 bond pdb=" C04 QUS A 901 " pdb=" N14 QUS A 901 " ideal model delta sigma weight residual 1.380 1.439 -0.059 2.00e-02 2.50e+03 8.56e+00 ... (remaining 13424 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 18165 2.76 - 5.52: 89 5.52 - 8.27: 10 8.27 - 11.03: 0 11.03 - 13.79: 2 Bond angle restraints: 18266 Sorted by residual: angle pdb=" C03 QUS A 901 " pdb=" N14 QUS A 901 " pdb=" O20 QUS A 901 " ideal model delta sigma weight residual 112.77 126.56 -13.79 3.00e+00 1.11e-01 2.11e+01 angle pdb=" C03 QUS B 901 " pdb=" N14 QUS B 901 " pdb=" O20 QUS B 901 " ideal model delta sigma weight residual 112.77 126.36 -13.59 3.00e+00 1.11e-01 2.05e+01 angle pdb=" N LEU B 567 " pdb=" CA LEU B 567 " pdb=" C LEU B 567 " ideal model delta sigma weight residual 107.88 112.63 -4.75 1.41e+00 5.03e-01 1.14e+01 angle pdb=" C MET B 817 " pdb=" N PHE B 818 " pdb=" CA PHE B 818 " ideal model delta sigma weight residual 122.50 116.94 5.56 1.82e+00 3.02e-01 9.32e+00 angle pdb=" N VAL A 191 " pdb=" CA VAL A 191 " pdb=" C VAL A 191 " ideal model delta sigma weight residual 111.91 109.24 2.67 8.90e-01 1.26e+00 8.98e+00 ... (remaining 18261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7239 17.99 - 35.98: 627 35.98 - 53.98: 101 53.98 - 71.97: 21 71.97 - 89.96: 13 Dihedral angle restraints: 8001 sinusoidal: 2891 harmonic: 5110 Sorted by residual: dihedral pdb=" CB CYS B 515 " pdb=" SG CYS B 515 " pdb=" SG CYS B 534 " pdb=" CB CYS B 534 " ideal model delta sinusoidal sigma weight residual -86.00 -7.00 -79.00 1 1.00e+01 1.00e-02 7.77e+01 dihedral pdb=" CB CYS A 511 " pdb=" SG CYS A 511 " pdb=" SG CYS A 531 " pdb=" CB CYS A 531 " ideal model delta sinusoidal sigma weight residual -86.00 -144.99 58.99 1 1.00e+01 1.00e-02 4.65e+01 dihedral pdb=" CB CYS B 241 " pdb=" SG CYS B 241 " pdb=" SG CYS B 530 " pdb=" CB CYS B 530 " ideal model delta sinusoidal sigma weight residual -86.00 -127.44 41.44 1 1.00e+01 1.00e-02 2.40e+01 ... (remaining 7998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1508 0.042 - 0.085: 411 0.085 - 0.127: 136 0.127 - 0.169: 9 0.169 - 0.212: 3 Chirality restraints: 2067 Sorted by residual: chirality pdb=" CB ILE A 636 " pdb=" CA ILE A 636 " pdb=" CG1 ILE A 636 " pdb=" CG2 ILE A 636 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE B 636 " pdb=" N ILE B 636 " pdb=" C ILE B 636 " pdb=" CB ILE B 636 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.99e-01 chirality pdb=" CA ILE B 642 " pdb=" N ILE B 642 " pdb=" C ILE B 642 " pdb=" CB ILE B 642 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.26e-01 ... (remaining 2064 not shown) Planarity restraints: 2356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 535 " -0.072 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO A 536 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO A 536 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 536 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 430 " -0.046 5.00e-02 4.00e+02 7.05e-02 7.94e+00 pdb=" N PRO A 431 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 431 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 431 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 64 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C TYR A 64 " 0.030 2.00e-02 2.50e+03 pdb=" O TYR A 64 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY A 65 " -0.010 2.00e-02 2.50e+03 ... (remaining 2353 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2162 2.76 - 3.30: 12377 3.30 - 3.83: 20866 3.83 - 4.37: 24112 4.37 - 4.90: 42971 Nonbonded interactions: 102488 Sorted by model distance: nonbonded pdb=" OH TYR A 311 " pdb=" OD1 ASP A 480 " model vdw 2.230 3.040 nonbonded pdb=" OE1 GLN D 15 " pdb=" OG SER D 124 " model vdw 2.267 3.040 nonbonded pdb=" OG1 THR B 559 " pdb=" OD1 ASP B 561 " model vdw 2.310 3.040 nonbonded pdb=" O ARG D 29 " pdb=" OG1 THR D 30 " model vdw 2.323 3.040 nonbonded pdb=" O ASP B 718 " pdb=" N ASN B 734 " model vdw 2.323 3.120 ... (remaining 102483 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 297 or (resid 298 and (name N or n \ ame CA or name C or name O or name CB )) or resid 299 through 490 or (resid 491 \ and (name N or name CA or name C or name O or name CB )) or resid 492 through 52 \ 3 or (resid 524 and (name N or name CA or name C or name O or name CB )) or resi \ d 525 through 545 or (resid 546 through 547 and (name N or name CA or name C or \ name O or name CB )) or resid 548 through 634 or (resid 635 through 638 and (nam \ e N or name CA or name C or name O or name CB )) or resid 639 through 901)) selection = (chain 'B' and (resid 25 through 417 or resid 428 through 501 or (resid 502 thro \ ugh 503 and (name N or name CA or name C or name O or name CB )) or resid 504 th \ rough 507 or (resid 508 and (name N or name CA or name C or name O or name CB )) \ or resid 509 through 512 or (resid 513 and (name N or name CA or name C or name \ O or name CB )) or resid 514 through 516 or (resid 517 and (name N or name CA o \ r name C or name O or name CB )) or resid 518 or (resid 519 and (name N or name \ CA or name C or name O or name CB )) or resid 520 through 541 or (resid 542 and \ (name N or name CA or name C or name O or name CB )) or resid 543 through 552 or \ (resid 553 and (name N or name CA or name C or name O or name CB )) or resid 55 \ 4 through 566 or (resid 567 and (name N or name CA or name C or name O or name C \ B )) or resid 568 through 901)) } ncs_group { reference = (chain 'C' and (resid 3 through 44 or (resid 45 and (name N or name CA or name C \ or name O or name CB )) or resid 46 through 116 or (resid 117 and (name N or na \ me CA or name C or name O or name CB )) or resid 118 through 125)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.570 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 0.003 0.076 13446 Z= 0.165 Angle : 0.564 13.792 18300 Z= 0.306 Chirality : 0.043 0.212 2067 Planarity : 0.005 0.109 2356 Dihedral : 14.005 89.959 4666 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.20), residues: 1752 helix: 1.71 (0.20), residues: 686 sheet: -0.05 (0.30), residues: 294 loop : -1.41 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 106 TYR 0.016 0.001 TYR A 223 PHE 0.019 0.001 PHE A 818 TRP 0.009 0.001 TRP A 336 HIS 0.004 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00306 (13429) covalent geometry : angle 0.56322 (18266) SS BOND : bond 0.00179 ( 17) SS BOND : angle 1.00318 ( 34) hydrogen bonds : bond 0.13012 ( 637) hydrogen bonds : angle 5.65136 ( 1836) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.499 Fit side-chains REVERT: A 524 ARG cc_start: 0.6176 (ttt-90) cc_final: 0.5781 (tpt-90) REVERT: C 85 MET cc_start: 0.7211 (mtt) cc_final: 0.6981 (mtp) REVERT: D 36 MET cc_start: 0.8451 (mmm) cc_final: 0.8140 (mmp) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.5612 time to fit residues: 84.7931 Evaluate side-chains 119 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN B 157 GLN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.161304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.111054 restraints weight = 19410.613| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.57 r_work: 0.3616 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13446 Z= 0.202 Angle : 0.601 13.688 18300 Z= 0.317 Chirality : 0.045 0.177 2067 Planarity : 0.005 0.078 2356 Dihedral : 5.268 75.616 1908 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.76 % Allowed : 8.71 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.20), residues: 1752 helix: 1.99 (0.20), residues: 686 sheet: -0.24 (0.29), residues: 299 loop : -1.47 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 465 TYR 0.022 0.002 TYR A 223 PHE 0.019 0.002 PHE A 818 TRP 0.011 0.001 TRP A 336 HIS 0.005 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00485 (13429) covalent geometry : angle 0.59887 (18266) SS BOND : bond 0.00308 ( 17) SS BOND : angle 1.19569 ( 34) hydrogen bonds : bond 0.05224 ( 637) hydrogen bonds : angle 4.47343 ( 1836) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.526 Fit side-chains REVERT: A 72 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.7835 (ttt) REVERT: A 494 MET cc_start: 0.9026 (ttp) cc_final: 0.8720 (ttm) REVERT: B 720 MET cc_start: 0.7579 (pmm) cc_final: 0.7355 (pmm) outliers start: 10 outliers final: 5 residues processed: 124 average time/residue: 0.6294 time to fit residues: 84.9685 Evaluate side-chains 125 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 105 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 129 optimal weight: 30.0000 chunk 30 optimal weight: 0.4980 chunk 136 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.163455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.113498 restraints weight = 19718.479| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.62 r_work: 0.3641 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13446 Z= 0.133 Angle : 0.532 14.710 18300 Z= 0.278 Chirality : 0.043 0.172 2067 Planarity : 0.004 0.064 2356 Dihedral : 4.933 82.969 1908 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.91 % Allowed : 11.28 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.20), residues: 1752 helix: 2.25 (0.20), residues: 682 sheet: -0.13 (0.29), residues: 299 loop : -1.41 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 465 TYR 0.014 0.001 TYR A 223 PHE 0.019 0.001 PHE A 818 TRP 0.010 0.001 TRP A 336 HIS 0.004 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00308 (13429) covalent geometry : angle 0.53081 (18266) SS BOND : bond 0.00201 ( 17) SS BOND : angle 1.00463 ( 34) hydrogen bonds : bond 0.04144 ( 637) hydrogen bonds : angle 4.13536 ( 1836) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.521 Fit side-chains REVERT: A 72 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.7760 (ttt) REVERT: A 802 MET cc_start: 0.6189 (pmm) cc_final: 0.5643 (pmm) REVERT: B 720 MET cc_start: 0.7536 (pmm) cc_final: 0.7124 (pmm) REVERT: C 111 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: D 85 MET cc_start: 0.7758 (mtt) cc_final: 0.7431 (mtm) outliers start: 12 outliers final: 3 residues processed: 123 average time/residue: 0.6574 time to fit residues: 87.9346 Evaluate side-chains 123 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 30 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 16 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 157 optimal weight: 0.7980 chunk 161 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.161196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.110744 restraints weight = 19423.641| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.60 r_work: 0.3613 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13446 Z= 0.188 Angle : 0.577 15.042 18300 Z= 0.303 Chirality : 0.044 0.190 2067 Planarity : 0.004 0.055 2356 Dihedral : 5.170 86.853 1908 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.74 % Allowed : 13.25 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.20), residues: 1752 helix: 2.14 (0.20), residues: 691 sheet: -0.12 (0.30), residues: 287 loop : -1.48 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 465 TYR 0.017 0.001 TYR B 223 PHE 0.018 0.002 PHE A 818 TRP 0.010 0.001 TRP A 336 HIS 0.004 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00454 (13429) covalent geometry : angle 0.57562 (18266) SS BOND : bond 0.00292 ( 17) SS BOND : angle 1.10335 ( 34) hydrogen bonds : bond 0.04721 ( 637) hydrogen bonds : angle 4.14993 ( 1836) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.384 Fit side-chains REVERT: A 72 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7825 (ttt) REVERT: A 720 MET cc_start: 0.7653 (pmm) cc_final: 0.7451 (pmm) REVERT: A 802 MET cc_start: 0.6169 (pmm) cc_final: 0.5629 (pmm) REVERT: B 72 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.7939 (ttt) REVERT: B 277 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.6665 (t80) REVERT: B 720 MET cc_start: 0.7568 (pmm) cc_final: 0.7327 (pmm) REVERT: C 111 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: D 85 MET cc_start: 0.7848 (mtt) cc_final: 0.7537 (mtm) outliers start: 23 outliers final: 7 residues processed: 130 average time/residue: 0.5234 time to fit residues: 73.8602 Evaluate side-chains 127 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 34 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 157 GLN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.172752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.114535 restraints weight = 20503.447| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.91 r_work: 0.3599 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13446 Z= 0.174 Angle : 0.561 14.948 18300 Z= 0.295 Chirality : 0.044 0.171 2067 Planarity : 0.004 0.050 2356 Dihedral : 5.115 86.935 1908 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.04 % Allowed : 13.70 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.20), residues: 1752 helix: 2.23 (0.20), residues: 687 sheet: -0.14 (0.29), residues: 299 loop : -1.44 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 465 TYR 0.016 0.001 TYR A 223 PHE 0.019 0.001 PHE A 544 TRP 0.011 0.001 TRP A 336 HIS 0.004 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00418 (13429) covalent geometry : angle 0.56020 (18266) SS BOND : bond 0.00272 ( 17) SS BOND : angle 1.04640 ( 34) hydrogen bonds : bond 0.04472 ( 637) hydrogen bonds : angle 4.07167 ( 1836) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.328 Fit side-chains REVERT: A 72 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7859 (ttt) REVERT: A 277 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7560 (t80) REVERT: A 720 MET cc_start: 0.7574 (pmm) cc_final: 0.7304 (pmm) REVERT: A 802 MET cc_start: 0.6236 (pmm) cc_final: 0.5696 (pmm) REVERT: B 72 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7905 (ttt) REVERT: B 277 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.6706 (t80) REVERT: B 291 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7111 (ttm170) REVERT: C 61 HIS cc_start: 0.8855 (OUTLIER) cc_final: 0.7640 (m-70) REVERT: C 111 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: D 85 MET cc_start: 0.7917 (mtt) cc_final: 0.7708 (mtt) outliers start: 27 outliers final: 8 residues processed: 132 average time/residue: 0.5345 time to fit residues: 76.8281 Evaluate side-chains 131 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 111 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 29 optimal weight: 1.9990 chunk 144 optimal weight: 30.0000 chunk 171 optimal weight: 7.9990 chunk 94 optimal weight: 0.0870 chunk 93 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.161424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.122099 restraints weight = 19373.450| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.53 r_work: 0.3547 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13446 Z= 0.175 Angle : 0.566 14.393 18300 Z= 0.297 Chirality : 0.044 0.171 2067 Planarity : 0.004 0.052 2356 Dihedral : 5.116 86.827 1908 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.04 % Allowed : 14.69 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.20), residues: 1752 helix: 2.27 (0.20), residues: 687 sheet: -0.09 (0.30), residues: 285 loop : -1.40 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 465 TYR 0.017 0.001 TYR A 223 PHE 0.018 0.001 PHE A 818 TRP 0.010 0.001 TRP A 336 HIS 0.004 0.001 HIS B 44 Details of bonding type rmsd covalent geometry : bond 0.00422 (13429) covalent geometry : angle 0.56420 (18266) SS BOND : bond 0.00271 ( 17) SS BOND : angle 1.17189 ( 34) hydrogen bonds : bond 0.04483 ( 637) hydrogen bonds : angle 4.02845 ( 1836) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.503 Fit side-chains REVERT: A 72 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7810 (ttt) REVERT: A 277 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7478 (t80) REVERT: A 546 GLU cc_start: 0.8179 (tp30) cc_final: 0.7970 (tp30) REVERT: A 720 MET cc_start: 0.7454 (pmm) cc_final: 0.7160 (pmm) REVERT: A 802 MET cc_start: 0.6183 (pmm) cc_final: 0.5658 (pmm) REVERT: B 72 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7912 (ttt) REVERT: B 277 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.6607 (t80) REVERT: B 291 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.6959 (ttm170) REVERT: B 498 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6598 (tp30) REVERT: C 61 HIS cc_start: 0.8766 (OUTLIER) cc_final: 0.7528 (m-70) REVERT: C 79 ASN cc_start: 0.7906 (OUTLIER) cc_final: 0.7636 (t0) REVERT: C 111 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7063 (mp0) outliers start: 27 outliers final: 10 residues processed: 136 average time/residue: 0.5420 time to fit residues: 80.5722 Evaluate side-chains 134 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 111 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 169 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 131 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.174719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.121169 restraints weight = 20368.757| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.15 r_work: 0.3573 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13446 Z= 0.194 Angle : 0.583 13.587 18300 Z= 0.306 Chirality : 0.044 0.172 2067 Planarity : 0.004 0.052 2356 Dihedral : 5.203 86.999 1908 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.04 % Allowed : 16.12 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.20), residues: 1752 helix: 2.27 (0.20), residues: 686 sheet: -0.18 (0.30), residues: 285 loop : -1.42 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 465 TYR 0.017 0.001 TYR A 223 PHE 0.022 0.002 PHE A 544 TRP 0.011 0.001 TRP A 336 HIS 0.004 0.001 HIS B 44 Details of bonding type rmsd covalent geometry : bond 0.00472 (13429) covalent geometry : angle 0.58148 (18266) SS BOND : bond 0.00305 ( 17) SS BOND : angle 1.21273 ( 34) hydrogen bonds : bond 0.04673 ( 637) hydrogen bonds : angle 4.02821 ( 1836) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.565 Fit side-chains REVERT: A 72 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.7899 (ttt) REVERT: A 277 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.7609 (t80) REVERT: A 720 MET cc_start: 0.7755 (pmm) cc_final: 0.7422 (pmm) REVERT: A 802 MET cc_start: 0.6137 (pmm) cc_final: 0.5599 (pmm) REVERT: B 72 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8008 (ttt) REVERT: B 277 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.6767 (t80) REVERT: B 291 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7146 (ttm170) REVERT: B 498 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6841 (tp30) REVERT: C 61 HIS cc_start: 0.8872 (OUTLIER) cc_final: 0.7659 (m-70) REVERT: C 79 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7851 (t0) REVERT: C 111 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: D 85 MET cc_start: 0.7771 (mtt) cc_final: 0.7556 (mtt) outliers start: 27 outliers final: 12 residues processed: 134 average time/residue: 0.5407 time to fit residues: 78.7891 Evaluate side-chains 136 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 111 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 71 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 117 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN D 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.173864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.120793 restraints weight = 20347.543| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.31 r_work: 0.3557 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13446 Z= 0.219 Angle : 0.606 13.756 18300 Z= 0.319 Chirality : 0.045 0.182 2067 Planarity : 0.004 0.051 2356 Dihedral : 5.315 87.656 1908 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.35 % Allowed : 16.43 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.20), residues: 1752 helix: 2.27 (0.20), residues: 683 sheet: -0.27 (0.29), residues: 285 loop : -1.46 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 465 TYR 0.019 0.002 TYR A 223 PHE 0.018 0.002 PHE A 818 TRP 0.011 0.001 TRP A 336 HIS 0.005 0.001 HIS B 44 Details of bonding type rmsd covalent geometry : bond 0.00536 (13429) covalent geometry : angle 0.60462 (18266) SS BOND : bond 0.00339 ( 17) SS BOND : angle 1.24874 ( 34) hydrogen bonds : bond 0.04905 ( 637) hydrogen bonds : angle 4.06630 ( 1836) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.326 Fit side-chains REVERT: A 72 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7916 (ttt) REVERT: A 277 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7618 (t80) REVERT: A 720 MET cc_start: 0.7783 (pmm) cc_final: 0.7436 (pmm) REVERT: A 802 MET cc_start: 0.6096 (pmm) cc_final: 0.5565 (pmm) REVERT: B 277 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.6716 (t80) REVERT: B 291 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7191 (ttm170) REVERT: B 474 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8521 (mmt) REVERT: B 498 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6784 (tp30) REVERT: C 61 HIS cc_start: 0.8875 (OUTLIER) cc_final: 0.7662 (m-70) REVERT: C 79 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7807 (t0) REVERT: C 111 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: D 85 MET cc_start: 0.7788 (mtt) cc_final: 0.7475 (mtm) outliers start: 31 outliers final: 15 residues processed: 133 average time/residue: 0.5660 time to fit residues: 82.0306 Evaluate side-chains 137 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 530 CYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 111 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 119 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 147 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 174 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS B 157 GLN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.175591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.118051 restraints weight = 20687.906| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.78 r_work: 0.3649 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13446 Z= 0.152 Angle : 0.560 13.234 18300 Z= 0.291 Chirality : 0.043 0.180 2067 Planarity : 0.004 0.043 2356 Dihedral : 5.058 86.699 1908 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.27 % Allowed : 16.96 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.20), residues: 1752 helix: 2.41 (0.20), residues: 680 sheet: -0.19 (0.30), residues: 282 loop : -1.37 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 465 TYR 0.015 0.001 TYR A 223 PHE 0.022 0.001 PHE A 544 TRP 0.011 0.001 TRP A 336 HIS 0.004 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00363 (13429) covalent geometry : angle 0.55907 (18266) SS BOND : bond 0.00236 ( 17) SS BOND : angle 1.05942 ( 34) hydrogen bonds : bond 0.04204 ( 637) hydrogen bonds : angle 3.93195 ( 1836) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.407 Fit side-chains REVERT: A 72 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7823 (ttt) REVERT: A 277 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7471 (t80) REVERT: A 720 MET cc_start: 0.7655 (pmm) cc_final: 0.7332 (pmm) REVERT: A 802 MET cc_start: 0.5942 (pmm) cc_final: 0.5419 (pmm) REVERT: B 277 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.6740 (t80) REVERT: B 291 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7084 (ttm170) REVERT: B 474 MET cc_start: 0.9035 (mmt) cc_final: 0.8391 (mmt) REVERT: C 61 HIS cc_start: 0.8845 (OUTLIER) cc_final: 0.7639 (m-70) REVERT: C 79 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7931 (t0) REVERT: C 111 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: D 85 MET cc_start: 0.7788 (mtt) cc_final: 0.7485 (mtm) outliers start: 30 outliers final: 16 residues processed: 134 average time/residue: 0.5379 time to fit residues: 78.8832 Evaluate side-chains 139 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 435 ARG Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 530 CYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 111 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 124 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 152 optimal weight: 0.0470 chunk 131 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.175281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.117628 restraints weight = 20516.894| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.76 r_work: 0.3632 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13446 Z= 0.173 Angle : 0.585 13.000 18300 Z= 0.304 Chirality : 0.044 0.207 2067 Planarity : 0.004 0.049 2356 Dihedral : 5.104 86.144 1908 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.89 % Allowed : 17.49 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.20), residues: 1752 helix: 2.34 (0.20), residues: 686 sheet: -0.18 (0.30), residues: 280 loop : -1.41 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 465 TYR 0.016 0.001 TYR B 223 PHE 0.021 0.001 PHE B 818 TRP 0.010 0.001 TRP A 336 HIS 0.004 0.001 HIS B 44 Details of bonding type rmsd covalent geometry : bond 0.00419 (13429) covalent geometry : angle 0.58332 (18266) SS BOND : bond 0.00271 ( 17) SS BOND : angle 1.10851 ( 34) hydrogen bonds : bond 0.04463 ( 637) hydrogen bonds : angle 3.94954 ( 1836) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.569 Fit side-chains REVERT: A 72 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7808 (ttt) REVERT: A 277 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7479 (t80) REVERT: A 720 MET cc_start: 0.7734 (pmm) cc_final: 0.7396 (pmm) REVERT: A 802 MET cc_start: 0.5904 (pmm) cc_final: 0.5388 (pmm) REVERT: B 277 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.6739 (t80) REVERT: B 291 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7086 (ttm170) REVERT: C 61 HIS cc_start: 0.8852 (OUTLIER) cc_final: 0.7654 (m-70) REVERT: C 79 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7912 (t0) REVERT: C 111 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: D 85 MET cc_start: 0.7764 (mtt) cc_final: 0.7461 (mtm) outliers start: 25 outliers final: 14 residues processed: 132 average time/residue: 0.6087 time to fit residues: 87.3012 Evaluate side-chains 137 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 506 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 530 CYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 803 CYS Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 79 ASN Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 111 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 133 optimal weight: 20.0000 chunk 155 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 147 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 chunk 103 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.175779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.118286 restraints weight = 20488.644| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.77 r_work: 0.3645 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13446 Z= 0.150 Angle : 0.568 12.552 18300 Z= 0.294 Chirality : 0.043 0.206 2067 Planarity : 0.004 0.048 2356 Dihedral : 4.994 85.330 1908 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.89 % Allowed : 17.41 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.20), residues: 1752 helix: 2.39 (0.20), residues: 686 sheet: -0.16 (0.30), residues: 282 loop : -1.36 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 465 TYR 0.014 0.001 TYR B 223 PHE 0.025 0.001 PHE A 544 TRP 0.011 0.001 TRP A 336 HIS 0.004 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00357 (13429) covalent geometry : angle 0.56707 (18266) SS BOND : bond 0.00235 ( 17) SS BOND : angle 1.02482 ( 34) hydrogen bonds : bond 0.04172 ( 637) hydrogen bonds : angle 3.88106 ( 1836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4510.82 seconds wall clock time: 77 minutes 22.84 seconds (4642.84 seconds total)