Starting phenix.real_space_refine on Mon Dec 30 13:25:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t8m_41099/12_2024/8t8m_41099.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t8m_41099/12_2024/8t8m_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_41099/12_2024/8t8m_41099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t8m_41099/12_2024/8t8m_41099.map" model { file = "/net/cci-nas-00/data/ceres_data/8t8m_41099/12_2024/8t8m_41099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t8m_41099/12_2024/8t8m_41099.cif" } resolution = 3.0 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 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 4, 'TYR:plan': 12, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 7, 'GLU:plan': 7, 'ARG:plan': 9} 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: {'GLN:plan1': 2, 'TYR:plan': 12, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 7, 'GLU:plan': 9, 'ARG:plan': 9} 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: 8.94, per 1000 atoms: 0.68 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: 3.31 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.65 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: 5.74 Time building geometry restraints manager: 3.89 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 826 or res \ id 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 826 or resid 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.940 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 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:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.440 ------------------------------------------------------------------------------- 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 13429 Z= 0.207 Angle : 0.563 13.792 18266 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), 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 TRP 0.009 0.001 TRP A 336 HIS 0.004 0.001 HIS A 218 PHE 0.019 0.001 PHE A 818 TYR 0.016 0.001 TYR A 223 ARG 0.008 0.000 ARG D 106 *********************** 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 : 1.514 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: 1.3736 time to fit residues: 208.2589 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 : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 70 optimal weight: 0.0670 chunk 137 optimal weight: 30.0000 chunk 53 optimal weight: 20.0000 chunk 83 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13429 Z= 0.368 Angle : 0.620 12.667 18266 Z= 0.328 Chirality : 0.046 0.192 2067 Planarity : 0.005 0.078 2356 Dihedral : 5.356 75.392 1908 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.76 % Allowed : 8.93 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.16 (0.20), residues: 1752 helix: 1.95 (0.20), residues: 686 sheet: -0.29 (0.28), residues: 299 loop : -1.50 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.006 0.001 HIS B 30 PHE 0.019 0.002 PHE A 818 TYR 0.023 0.002 TYR A 223 ARG 0.008 0.001 ARG A 465 *********************** 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 130 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 1.531 Fit side-chains REVERT: A 72 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7703 (ttt) REVERT: A 494 MET cc_start: 0.8617 (ttp) cc_final: 0.8302 (ttm) outliers start: 10 outliers final: 5 residues processed: 123 average time/residue: 1.4198 time to fit residues: 191.0815 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 : 1.473 ------------------------------------------------------------------------------- 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 88 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 108 optimal weight: 0.0050 chunk 43 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 157 optimal weight: 0.4980 chunk 54 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 overall best weight: 1.3000 ------------------------------------------------------------------------------- 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** C 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13429 Z= 0.302 Angle : 0.581 14.415 18266 Z= 0.306 Chirality : 0.044 0.172 2067 Planarity : 0.004 0.064 2356 Dihedral : 5.264 85.873 1908 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.36 % Allowed : 12.19 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.21 (0.20), residues: 1752 helix: 2.05 (0.20), residues: 686 sheet: -0.30 (0.29), residues: 299 loop : -1.51 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.004 0.001 HIS B 44 PHE 0.018 0.002 PHE A 818 TYR 0.017 0.001 TYR A 223 ARG 0.008 0.000 ARG A 465 *********************** 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 137 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.679 Fit side-chains REVERT: A 72 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7646 (ttt) REVERT: A 802 MET cc_start: 0.5881 (pmm) cc_final: 0.5662 (pmm) REVERT: B 277 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.6744 (t80) REVERT: C 111 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6697 (mp0) outliers start: 18 outliers final: 8 residues processed: 126 average time/residue: 1.4409 time to fit residues: 197.8233 Evaluate side-chains 128 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 435 ARG Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 177 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 159 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13429 Z= 0.222 Angle : 0.544 15.220 18266 Z= 0.284 Chirality : 0.043 0.172 2067 Planarity : 0.004 0.053 2356 Dihedral : 5.053 88.396 1908 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.51 % Allowed : 13.40 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.20), residues: 1752 helix: 2.26 (0.20), residues: 681 sheet: -0.18 (0.29), residues: 299 loop : -1.43 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.004 0.001 HIS A 218 PHE 0.019 0.001 PHE A 818 TYR 0.014 0.001 TYR A 223 ARG 0.009 0.000 ARG A 465 *********************** 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: 20 poor density : 121 time to evaluate : 1.786 Fit side-chains REVERT: A 72 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7642 (ttt) REVERT: A 80 ASN cc_start: 0.8133 (p0) cc_final: 0.7866 (p0) REVERT: A 802 MET cc_start: 0.5874 (pmm) cc_final: 0.5645 (pmm) REVERT: C 111 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6655 (mp0) outliers start: 20 outliers final: 6 residues processed: 131 average time/residue: 1.3622 time to fit residues: 195.1969 Evaluate side-chains 126 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 435 ARG Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain D residue 30 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 144 optimal weight: 20.0000 chunk 116 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 13429 Z= 0.372 Angle : 0.615 14.770 18266 Z= 0.323 Chirality : 0.045 0.178 2067 Planarity : 0.004 0.054 2356 Dihedral : 5.355 88.376 1908 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.04 % Allowed : 14.76 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.26 (0.20), residues: 1752 helix: 2.08 (0.20), residues: 691 sheet: -0.25 (0.29), residues: 285 loop : -1.49 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.005 0.001 HIS B 30 PHE 0.019 0.002 PHE C 31 TYR 0.020 0.002 TYR B 223 ARG 0.010 0.000 ARG A 465 *********************** 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 142 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 1.505 Fit side-chains REVERT: A 72 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7685 (ttt) REVERT: A 277 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7542 (t80) REVERT: A 802 MET cc_start: 0.5921 (pmm) cc_final: 0.5686 (pmm) REVERT: B 72 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7804 (ttt) REVERT: B 277 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.6858 (t80) REVERT: C 61 HIS cc_start: 0.8928 (OUTLIER) cc_final: 0.7865 (m-70) REVERT: C 111 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6765 (mp0) outliers start: 27 outliers final: 11 residues processed: 130 average time/residue: 1.3749 time to fit residues: 195.6861 Evaluate side-chains 131 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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 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 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 111 GLU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 169 optimal weight: 0.1980 chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13429 Z= 0.244 Angle : 0.551 13.772 18266 Z= 0.289 Chirality : 0.043 0.171 2067 Planarity : 0.004 0.047 2356 Dihedral : 5.096 88.037 1908 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.12 % Allowed : 15.29 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.35 (0.20), residues: 1752 helix: 2.19 (0.20), residues: 691 sheet: -0.28 (0.29), residues: 301 loop : -1.47 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.004 0.001 HIS A 218 PHE 0.018 0.001 PHE A 818 TYR 0.015 0.001 TYR A 223 ARG 0.010 0.000 ARG A 465 *********************** 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: 28 poor density : 118 time to evaluate : 1.579 Fit side-chains REVERT: A 72 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7636 (ttt) REVERT: A 277 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7457 (t80) REVERT: A 802 MET cc_start: 0.5923 (pmm) cc_final: 0.5683 (pmm) REVERT: B 277 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.6856 (t80) REVERT: B 291 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7416 (ttm170) REVERT: C 61 HIS cc_start: 0.8900 (OUTLIER) cc_final: 0.7828 (m-70) REVERT: C 111 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6675 (mp0) outliers start: 28 outliers final: 11 residues processed: 135 average time/residue: 1.3130 time to fit residues: 194.3307 Evaluate side-chains 132 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.523 ------------------------------------------------------------------------------- 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 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 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 111 GLU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 142 optimal weight: 9.9990 chunk 94 optimal weight: 0.0470 chunk 168 optimal weight: 2.9990 chunk 105 optimal weight: 0.4980 chunk 102 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13429 Z= 0.173 Angle : 0.522 14.166 18266 Z= 0.272 Chirality : 0.042 0.172 2067 Planarity : 0.004 0.046 2356 Dihedral : 4.829 85.663 1908 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.97 % Allowed : 16.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.20), residues: 1752 helix: 2.43 (0.20), residues: 685 sheet: -0.11 (0.29), residues: 299 loop : -1.40 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.004 0.001 HIS A 218 PHE 0.020 0.001 PHE A 544 TYR 0.014 0.001 TYR B 542 ARG 0.011 0.000 ARG A 465 *********************** 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 149 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 1.487 Fit side-chains REVERT: A 72 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7571 (ttt) REVERT: A 802 MET cc_start: 0.5761 (pmm) cc_final: 0.5514 (pmm) REVERT: B 228 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8050 (mmp) REVERT: B 277 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.6839 (t80) REVERT: B 291 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7325 (ttm170) REVERT: C 61 HIS cc_start: 0.8874 (OUTLIER) cc_final: 0.7714 (m-70) REVERT: C 111 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6588 (mp0) outliers start: 26 outliers final: 10 residues processed: 138 average time/residue: 1.3119 time to fit residues: 198.3561 Evaluate side-chains 134 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 435 ARG Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain B residue 228 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 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 111 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.0970 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13429 Z= 0.193 Angle : 0.535 13.585 18266 Z= 0.277 Chirality : 0.042 0.171 2067 Planarity : 0.004 0.048 2356 Dihedral : 4.782 84.100 1908 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.74 % Allowed : 17.34 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.64 (0.20), residues: 1752 helix: 2.49 (0.20), residues: 684 sheet: -0.06 (0.29), residues: 299 loop : -1.35 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.004 0.001 HIS A 218 PHE 0.017 0.001 PHE A 818 TYR 0.012 0.001 TYR A 547 ARG 0.011 0.000 ARG A 465 *********************** 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 142 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 1.521 Fit side-chains REVERT: A 72 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7576 (ttt) REVERT: A 802 MET cc_start: 0.5771 (pmm) cc_final: 0.5513 (pmm) REVERT: B 228 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8106 (mmp) REVERT: B 277 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.6853 (t80) REVERT: B 291 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7363 (ttm170) REVERT: C 61 HIS cc_start: 0.8882 (OUTLIER) cc_final: 0.7728 (m-70) REVERT: C 111 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6608 (mp0) outliers start: 23 outliers final: 10 residues processed: 131 average time/residue: 1.3358 time to fit residues: 192.1268 Evaluate side-chains 135 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 435 ARG Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain B residue 228 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 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 111 GLU Chi-restraints excluded: chain D residue 30 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 94 optimal weight: 0.0030 chunk 68 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 148 optimal weight: 0.0970 chunk 156 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.4194 ------------------------------------------------------------------------------- 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 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13429 Z= 0.329 Angle : 0.605 12.742 18266 Z= 0.317 Chirality : 0.044 0.202 2067 Planarity : 0.004 0.054 2356 Dihedral : 5.144 85.317 1908 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.27 % Allowed : 17.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.20), residues: 1752 helix: 2.32 (0.20), residues: 685 sheet: -0.18 (0.30), residues: 285 loop : -1.39 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.004 0.001 HIS B 44 PHE 0.022 0.002 PHE A 544 TYR 0.018 0.002 TYR B 223 ARG 0.011 0.001 ARG A 465 *********************** 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 : 1.449 Fit side-chains REVERT: A 72 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7650 (ttt) REVERT: A 277 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7486 (t80) REVERT: A 802 MET cc_start: 0.5922 (pmm) cc_final: 0.5633 (pmm) REVERT: B 277 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.6838 (t80) REVERT: B 291 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7498 (ttm170) REVERT: B 474 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8091 (mmt) REVERT: C 61 HIS cc_start: 0.8922 (OUTLIER) cc_final: 0.7774 (m-70) REVERT: C 111 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6679 (mp0) outliers start: 30 outliers final: 12 residues processed: 134 average time/residue: 1.2586 time to fit residues: 184.8431 Evaluate side-chains 134 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.551 ------------------------------------------------------------------------------- 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 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 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 111 GLU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 174 optimal weight: 0.9980 chunk 160 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 chunk 14 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 0.0970 chunk 110 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13429 Z= 0.186 Angle : 0.551 12.541 18266 Z= 0.283 Chirality : 0.042 0.180 2067 Planarity : 0.004 0.043 2356 Dihedral : 4.844 84.018 1908 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.59 % Allowed : 18.09 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.58 (0.20), residues: 1752 helix: 2.41 (0.20), residues: 690 sheet: -0.15 (0.30), residues: 296 loop : -1.36 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.004 0.001 HIS A 218 PHE 0.018 0.001 PHE A 818 TYR 0.013 0.001 TYR A 547 ARG 0.010 0.000 ARG A 465 ********************** 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 137 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.501 Fit side-chains REVERT: A 72 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7540 (ttt) REVERT: A 802 MET cc_start: 0.5775 (pmm) cc_final: 0.5489 (pmm) REVERT: B 228 MET cc_start: 0.8586 (tpp) cc_final: 0.8092 (mmp) REVERT: B 277 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.6858 (t80) REVERT: B 291 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7328 (ttm170) REVERT: B 474 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8197 (mmt) REVERT: C 61 HIS cc_start: 0.8877 (OUTLIER) cc_final: 0.7714 (m-70) REVERT: C 111 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6651 (mp0) outliers start: 21 outliers final: 13 residues processed: 128 average time/residue: 1.4237 time to fit residues: 198.9890 Evaluate side-chains 135 residues out of total 1523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 435 ARG Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 261 LEU 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 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 111 GLU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 32 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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** D 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.173553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.119928 restraints weight = 20427.341| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.27 r_work: 0.3565 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 13429 Z= 0.403 Angle : 0.648 12.482 18266 Z= 0.337 Chirality : 0.046 0.220 2067 Planarity : 0.004 0.058 2356 Dihedral : 5.290 85.732 1908 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.74 % Allowed : 17.94 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.20), residues: 1752 helix: 2.30 (0.20), residues: 684 sheet: -0.26 (0.29), residues: 285 loop : -1.43 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 336 HIS 0.005 0.001 HIS B 44 PHE 0.030 0.002 PHE A 544 TYR 0.020 0.002 TYR B 223 ARG 0.013 0.001 ARG A 465 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3990.37 seconds wall clock time: 73 minutes 21.59 seconds (4401.59 seconds total)